Based on the efficient thermoelectric conversion capability of Stirling engine, the Autonomous Circulation Micro Integrated Nuclear Reactor (ACMIR) is highly integrated and lightweight, making it an attractive candidate for deep space exploration. However, in the applicability and safety demonstration of each application scenario, ACMIR faces the problem of lack of multi-parameter physically coupled simulation and computational models and modeling methods. Therefore, this study considers the heat source structure of the reactor core built into a Stirling engine and establishes a refined thermodynamic model of the system. By considering the reciprocating motion of the displacer piston and power piston in the Stirling engine, a dynamic model of the pistons is established. Subsequently, transient neutron dynamics is utilized for coupled solution to complete the multi-physics parameter coupling calculation of “nuclear-thermal-power” in the ACMIR. Through the rational selection of mathematical algorithms for solving the model, a preliminary analysis of the characteristics of the ACMIR under different load conditions is conducted. The results indicate that the established simulation model can basically align with the operational status of the space reactor system under various mission conditions. The developed model can serve as a research reference for the next step in system control.