The interchange between the Tsuen Wan Line and the Kwun Tong Line, the Island Line and the Tseung Kwan O Line, as well as that between the Kwun Tong Line and the Tseung Kwan O Line, are two stations long, allowing cross-platform interchange wherein a passenger leaves a train on one side of the platform and boards trains on the other side of the platform for another line. For example, when passengers are travelling on the Kwun Tong Line towards Tiu Keng Leng, getting off at Yau Tong would allow them to switch trains across the platform for the Tseung Kwan O Line towards North Point. Whereas, staying on the train and reaching Tiu Keng Leng would allow them to board the Tseung Kwan O Line trains towards Po Lam/LOHAS Park. This design makes interchanging more convenient and passengers do not have the need to change to different levels. However this interchange arrangement is not available for all transferring passengers at Kowloon Tong, Central, Hong Kong, Nam Cheong (Except transfer between Tuen Mun and Hong Kong bound trains), Mei Foo, Tai Wai Station (Except alighting from Ma On Shan Line to change southbound trains for East Rail Line) and Sunny Bay (Except alighting from Tung Chung bound trains to Disneyland Resort Line) stations, mainly because this service is available only when there are two continuous stations shared as interchange stations by two lines.
Two major works were undertaken to facilitate interchange between Kwun Tong Line and East Rail Line. The modification of Kowloon Tong Station started in June 2001. A new pedestrian link to Kowloon Tong Station southern concourse and a new entrance (Exit D) were opened on 15 April 2004 to cope with the increase in interchange passenger flow. Modification to Tsim Sha Tsui Station involved upgrading station facilities and concourse layout to facilitate access from the East Tsim Sha Tsui Station via its pedestrian links. New entrances to the subway links were opened on 19 September 2004 (Exit G) and 30 March 2005 (Exit F), with the whole scheme completed in May 2005.
The Ma On Shan Line was constructed by the KCR to serve Ma On Shan and City One residential areas and operation of the line was outsourced to the MTR. The system mostly runs on a viaduct between the middle of roads with stations, stopping right next to major buildings. The only time the trains don't run on viaducts is when the railway meets the route 2 highway, where it runs in the middle and then raises back to a viaduct. The railway is slightly different from all other Hong Kong railways because the trains run on the right, not the left; this is so that passengers can easily interchange from the Ma On Shan line to the East Rail Line towards Hong Hum. The majority of passengers using the line get off the train at Tai Wai to interchange to the East Rail Line, using the line as a feeder route.
The Disneyland Resort Line, previously known as Penny's Bay Rail Link, provides service to the Hong Kong Disneyland Resort which was opened on 12 September 2005. Service to Sunny Bay station on the Tung Chung Line started in 2005. The new line and the Disneyland Resort station opened on 1 August 2005. It is a 3.5–kilometre single-track railway that runs between Sunny Bay station and Disneyland Resort station. The Disneyland Resort station itself was designed to blend in with the ambience of the resort. The line currently operates fully automated, trains running every four to ten minutes without a driver, and the carriages were changed from the existing M-Train rolling stock to match the recreational and adventurous nature of the 3.5-minute journey.
The new AsiaWorld-Expo Station is an extension of the Airport Express serving the new international exhibition centre, known as the AsiaWorld-Expo at Hong Kong International Airport. The station opened on 20 December 2005 along with the exhibition centre. To cope with the projected increase in patronage, Airport Express trains have been expanded to utilise eight carriages from the previous seven. Additional trains will also be deployed on the Tung Chung line during major exhibitions and events.
On 5 October 2000, the operator of the MTR network, MTR Corporation Limited (MTRCL), became Hong Kong's first rail company to be privatised, marking the beginning of the Hong Kong government's initiative to dissolve its interests in public utilities. Prior to its listing on the Hong Kong Stock Exchange, the Mass Transit Railway Corporation (MTRC) was wholly owned by the Hong Kong government. The offering involved the sale of about one billion shares, and the company now has the largest shareholder base of any company listed in Hong Kong. In June 2001, MTRCL was transferred to the Hang Seng Index.
MTRCL has often developed properties next to stations to complement its already profitable railway business. Many recently built stations were incorporated into large housing estates or shopping complexes. For example, Tsing Yi station is built next to the Maritime Square shopping centre and directly underneath the Tierra Verde housing estate.
On 11 April 2006, MTRCL signed a non-binding memorandum of understanding with the Hong Kong government, the owner of Kowloon-Canton Railway Corporation, to merge the operation of the two railway networks in Hong Kong in spite of the strong opposition by the KCRC staff. The minority shareholders of the corporation approved the proposal at an extraordinary general meeting on 9 October 2007, allowing MTRCL to take over the operation of the KCR network and combine the fare system of the two networks on 2 December 2007.
On 2 December 2007 the Kowloon-Canton Railway Corporation (KCRC) granted a 50-year service concession (which may be extended) of the KCR network to MTRCL, in return for making annual payments to KCRC, thereby merging the railway operations of the two corporations under MTRCL's management. At the same time MTRCL changed its Chinese name from "地鐵有限公司" (Subway Limited Company) to "香港鐵路有限公司" (Hong Kong Railway Limited Company), but left its English name unchanged. After the merger, the MTR network included three more lines, East Rail Line, West Rail Line and Ma On Shan Line, as well as the Light Rail network and Guangdong Through Train to Guangzhou.
On 28 September 2008, fare zones of all commuter lines which is ex-KCR were merged. A passenger could travel on these networks with only one ticket, except where a transfer is made between Tsim Sha Tsui and East Tsim Sha Tsui stations, where two tickets are required. Student discounts on Octopus Card were also issued.
Various campaigns and activities are taken to help ensure that the MTR is a safe system to travel on. Poster campaigns displaying information on topics such as escalator safety are a common sight in all MTR stations, and announcements are made regularly as safety reminders to travelling passengers.
Bylaws have been recently introduced to deter potentially dangerous actions on the MTR, such as the ban of flammable goods on the MTR and rushing into trains when the doors are closing. Penalties ranging from fines to imprisonment have been imposed for such offenses. Metallic balloons are also banned due to previous incidents on KCR and on MTR's Island Line where a metallic balloon interfered with the operation of the overhead power lines.
Police officers patrol on trains and stations, and police posts are available at some stations. The Hong Kong Police Force has a Railway District responsible for the MTR and the KCR. Closed-circuit television cameras are installed in stations.