This paper is aiming to estimate the mutual influence of the stack cooling performances with the operation modes of the thermal management system for the hydrogen fuel cell vehicles. The heat capacity of the thermal management system was measured by varying the operating modes such as stack cooling heat exchanger only (Mode 1), stack cooling and electric devices cooling heat exchangers (Mode 2), and stack cooling and electric devices cooling heat exchangers with an operation of the condenser (Mode 3).As the results, Performance of the thermal management system (TMS) at Mode 3 decreased up to 34.0%, compared with the result of the Mode 1. In addition, in order to optimize the performance of TMS, the entropy change of stack cooling heat exchanger using irreversibility analysis technique was analyzed with the relationship between entropy generation and entering air velocity of the thermal management system.