A data transferring method based on a protection and control system for an intelligent substation, wherein merging unit and intelligent terminal integrated devices for all bays in the intelligent substation are directly accessed to an intelligent power server, each of the merging unit and intelligent terminal integrated devices is accessed to one of transport ports of a field-programmable gate array FPGA access chip on the intelligent power server through a physical link, and the merging unit and intelligent terminal integrated devices and the transport ports are in a relationship of one-to-one correspondence, wherein the intelligent power server is configured to realize all functions of measurement and control, protection, switching and telecontrol in the intelligent substation, and the method comprises: in a reception period of a real-time business central processor of the intelligent power server, reading, by the real-time business central processor, at least one of sampled value SV messages and generic object oriented substation events GOOSE messages transmitted by each of the merging unit and intelligent terminal integrated devices from each reception buffer clip of the FPGA access chip, wherein the SV messages or the GOOSE messages are received from each of the transport ports by the FPGA access chip, subjected to a SV processing or GOOSE processing, and then written into corresponding reception buffer clips in a reception buffer, wherein the reception buffer clips and the transport ports are in a relationship of one-to-one correspondence; in a transmission period of the real-time business central processor, issuing, by the real-time business central processor, indication information generated in at least one of a measurement and control process and a protection process to the FPGA access chip, causing the FPGA access chip to generate the GOOSE messages according to the indication information and write the GOOSE messages into a transmission buffer of the FPGA access chip; wherein the step of reading, by the real-time business central processor, at least one of SV messages and GOOSE messages transmitted by each of the merging unit and intelligent terminal integrated devices from each reception buffer clip of the FPGA access chip comprises: reading, by the real-time business central processor, messages from each reception buffer clip according to a descending order of a total number of messages in each reception buffer clip, wherein the FPGA access chip reports the total number of messages in each reception buffer clip to the real-time business central processor in the reception period. in a reception period of a real-time business central processor of the intelligent power server, reading, by the real-time business central processor, at least one of sampled value SV messages and generic object oriented substation events GOOSE messages transmitted by each of the merging unit and intelligent terminal integrated devices from each reception buffer clip of the FPGA access chip, wherein the SV messages or the GOOSE messages are received from each of the transport ports by the FPGA access chip, subjected to a SV processing or GOOSE processing, and then written into corresponding reception buffer clips in a reception buffer, wherein the reception buffer clips and the transport ports are in a relationship of one-to-one correspondence; in a transmission period of the real-time business central processor, issuing, by the real-time business central processor, indication information generated in at least one of a measurement and control process and a protection process to the FPGA access chip, causing the FPGA access chip to generate the GOOSE messages according to the indication information and write the GOOSE messages into a transmission buffer of the FPGA access chip;