The performance of a fuel cell stack is affected by the operating temperature of the stack. The thermal management subsystem of a multi-stack fuel cell system (MFCS) is particularly significant for the operating temperature control of each stack in the MFCS. To study the influence of different topologies of a MFCS thermal management subsystem, this paper proposes and establishes two different topologies. Firstly, the integrated topology is proposed. Secondly, seven component models, namely the mixer, thermostat, radiator, tank, pump, bypass value, and proton exchange membrane fuel cell stack temperature models, are described in detail. Finally, the performance of the two topologies of the MFCS thermal management subsystem under two working conditions, steady (200 A) and variable (China heavy-duty commercial test cycle, C-WTVC), is compared. Furthermore, there are two evaluating indicators, including the stability duration and deviation of the operating temperatures of the single stack in the MFCS. Results show that when the MFCS operates under steady working conditions, the integrated topology is superior in operating temperature control accuracy (ΔT<0.5 K), while the distributed topology is superior in the adjustment process (t ≤ 100 s). Moreover, when the MFCS operates under variable working conditions, the distributed topology is superior in operating temperature control accuracy.