The invention provides a natural gas fuel cell power generation system and method adopting a supercritical CO2 bottom cycle. The system comprises a fuel reformer, a fuel cell, a cathode air compressor, an anode heat regenerator, a cathode heat feeding regenerator, an air turbine, a compressor, a waste heat boiler, a pure oxygen burner, a regenerator, a CO2 cooling and pressurizing device and a steam turbine; by adopting the structure, the power generation efficiency is further improved on the basis of high-efficiency power generation of a fuel cell; meanwhile, the bottom cycle adopts a supercritical carbon dioxide cycle power generation system, so that the system is simple and the equipment volume is greatly reduced; and the system also takes into account a CO2 capture function, and can realize the CO2 emission reduction of coal power generation efficiently at low cost.