The thermoelectric generation system of main engine waste heat is an important auxiliary system in the field of waste heat power generation. In order to confirm the feasibility of the thermoelectric generation system for ship waste heat power generation,the dynamic process of thermoelectric conversion should be analyzed and the adaptability should be tested with different conditions of this system. A dynamic mathematic model was established by analyzing the thermoelectric conversion process using thermoelectric conversion theory. And the parameters fluctuation was considered by adding the auxiliary boost converter part. The analysis of the simulation result on SIMULINK shows that the system is stable and feasible in different work conditions for waste heat power generation.