Abstract Fuel cell power technology has drawn extensive attentions due to its high efficiency, low emission and noise. Solid oxide fuel cell (SOFC) could generate the power by diverse fuels, such as natural gas (NG), while proton exchange membrane fuel cell (PEMFC) only feeds on pure H2. More and more attentions are paid on the combination of SOFC and PEMFC for high efficiency and convenient refueling in the practical applications. To obtain H2 fuel with high purity from SOFC as a reformer, the gas processing subsystem for H2 separation and purification should be applied between SOFC and PEMFC. In this present study, the gas processing subsystem, consisting of water gas shift (WGS) and thermal swing adsorption (TSA), is introduced into the SOFC-PEMFC hybrid system. Then, the SOFC-WGS-TSA-PEMFC hybrid system is modelled to investigate the transient behaviors under different operations. The simulation results show that the SOFC-WGS-TSA-PEMFC hybrid system has an improved energy conversion efficiency of approximately 64%, which is higher than the only-SOFC and the reform-PEMFC. The waste heat recovery for driving the TSA reaction accounts for the higher net electricity efficiency compared with the SOFC-PEMFC hybrid system based on the pressure swing adsorption (PSA) for H2 separation. Since the SOFC and PEMFC have completely different transient responses to the change of the loading, the influences of operating conditions of fuel cell vehicles on the transient behaviors of single SOFC and PEMFC and the overall performance of the SOFC-WGS-TSA-PEMFC hybrid system are further investigated. Through the analysis and discussion based on the dynamic modelling, the operation strategy is unveiled in this paper for the performance optimization of the hybrid system when installed in the fuel cell vehicles.