Due to the physical coupling in thermodynamic and mechanical systems, a new modeling methodology was offered based on power-bond graph. Power-bond graph was ideally suitable for multiple energy domains. As a fact, there are three forms of energy exchange in thermodynamic system, such as mechanical work, heat transfer and mass flow. Accordingly, three power ports of thermal C-field were analyzed to find out the thermal bond graph model. Afterwards, the model of mechanical translation and rotation was also figured out similarly but comparatively easier. On principle of bond graph, the normal state equation was deduced, from the simulation model describing the whole working process. Based on the model and the structure parameters of an actual diesel engine, the sound simulation result is achieved, verifying the validity of the methodology.