The global warming potential (GWP) of $CO_2$ refrigerant is 1/1300 times lower than that of R134a. Furthermore, the size and weight of the automotive heat pump system can decrease because $CO_2$ operates at high pressure with significantly higher discharge temperature and larger temperature change. The presented $CO_2$ heat pump system was designed for both cooling and heating in fuel cell vehicles. In this study, the performance characteristics of the heat pump system were analyzed for heating, and results for performance were provided for operating conditions when using recovered heat from the stack coolant. The performance of the heat pump system with heater core was compared with that of the conventional heating system with heater core and that of the heat pump system without heater core, and thus the heat pump system with heater core showed the best performance among the selected heating systems. On the other hand, the heating performance of two different types of coolant/air heat pump systems with heater core was compared each other at various coolant inlet temperatures. Furthermore, to use exhausted thermal energy through the radiator, experiments were carried out by changing the arrangement of a radiator and an outdoor evaporator, and quantified the heating effectiveness.