The piston motion of the opposed piston and opposed cylinder two-stroke engine is different from the traditional engine because of the special structure of inner and outer connecting rods. Based on the theory of equal cubage change ration, and compared with the performance analysis method of traditional structure engine, how to use BOOST software to analyze the opposed piston and opposed cylinder two-stroke engine and its feasibility are discussed. The research show that this method is feasible; as the piston motion rule of this engine is different, its P-V figure is more well-developed, and can help to improve the heat efficiency; however, at the same time, the highest combustion temperature goes higher, and resulted in thermal load increasing.