By the year 2045, it is projected that Autonomous Vehicles (AVs) will make up half of the new vehicle market. Successful adoption of AVs can reduce drivers' stress and fatigue, curb traffic congestion, and improve safety, mobility, and economic efficiency. Due to the limited intelligence in relevant technologies, human-in-the-loop modalities are still necessary to ensure the safety of AVs at current or near future stages, because the vehicles may not be able to handle all emergencies. Therefore, it is important to know the takeover readiness of the drivers to ensure the takeover quality and avoid any potential accidents. To achieve this, a comprehensive understanding of the drivers' physiological states is crucial. However, there is a lack of systematic analysis of the correlation between different human physiological responses and takeover behaviors which could serve as important references for future studies to determine the types of data to use. This paper provides a comprehensive analysis of the effects of takeover behaviors on the common physiological indicators. A program for conditional automation was developed based on a game engine and applied to a driving simulator. The experiment incorporated three types of secondary tasks, three takeover events, and two traffic densities. Brain signals, Skin Conductance Level (SCL), and Heart Rate (HR) of the participants were collected while they were performing the driving simulations. The Frontal Asymmetry Index (FAI) (as an indicator of engagement) and Mental Workload (MWL) were calculated from the brain signals to indicate the mental states of the participants. The results revealed that the FAI of the drivers would slightly decrease after the takeover alerts were issued when they were doing secondary tasks prior to the takeover activities, and the higher difficulty of the secondary tasks could lead to lower overall FAI during the takeover periods. In contrast, The MWL and SCL increased during the takeover periods. The HR also increased rapidly at the beginning of the takeover period but dropped back to a normal level quickly. It was found that a fake takeover alert would lead to lower overall HR, slower increase, and lower peak of SCL during the takeover periods. Moreover, the higher traffic density scenarios were associated with higher MWL, and a more difficult secondary task would lead to higher MWL and HR during the takeover activities. A preliminary discussion of the correlation between the physiological data, takeover scenario, and vehicle data (that relevant to takeover readiness) was then conducted, revealing that although takeover event, SCL, and HR had slightly higher correlations with the maximum acceleration and reaction time, none of them dominated the takeover readiness. In addition, the analysis of the data across different participants was conducted, which emphasized the importance of considering standardization or normalization of the data when they were further used as input features for estimating takeover readiness. Overall, the results presented in this paper offer profound insights into the patterns of physiological data changes during takeover periods. These findings can be used as benchmarks for utilizing these variables as indicators of takeover preparedness and performance in future research endeavors.