The invention discloses an automotive fuel cell combined heat and power generation system. The system mainly comprises a natural gas tank (1), a natural gas compressor (2), an air compressor (3), an air preheater (4), a natural gas reformer (5), a solid oxide fuel cell stack (6), a combustor (9), a water evaporator (10) and a water tank (11). The invention further provides a working method on the basis of the automotive fuel cell combined heat and power generation system. According to the working method, the hydrogen ions in the natural gas are separated by the natural gas reformer (5) to form hydrogen, the hydrogen and high-temperature air passing through the air preheater (4) generate electrochemical reaction in the solid oxide fuel cell stack (6), and the hydrogen and oxygen, which do not generate electrochemical reaction, generate hot gas through the combustor (9). According to the automotive fuel cell combined heat and power generation system and the working method thereof, the natural gas not only can be used for providing power for the vehicles through natural gas engines, but also can generate electric energy and heat energy when the natural gas engines do not work, so as to satisfy certain special purposes.