The $CO_2$ air conditioning system installed in fuel cell vehicles could be used either for stack cooling or for cabin cooling, and thus was used for the stack cooling when additional stack heat release was required over a fixed radiator capacity for high power generation. This study investigated the performance of the stack cooling system using $CO_2$ air conditioner at various operating conditions. Also, the heat releasing effectiveness and mutual interference were analyzed for the stack cooling system using an air conditioner and compared with the conventional radiator cooling system with/without cabin cooling. The heat release of the stack cooling system with the aid of $CO_2$ air conditioner increased up to 36% more than that of the conventional radiator cooling system with cabin cooling. Furthermore, the heat release of the stack cooling system using $CO_2$ air conditioner increased more by 7% than that of the conventional radiator cooling system without cabin cooling.