Abstract: The output performance of a free-piston Stirling engine is affected by multiple parameters. Analyzing the internal heat exchanger structure and thermodynamic parameters of a free-piston Stirling engine can aid in optimizing the engine design and enhancing thermal performance. In this study, a thermodynamic model of a free-piston Stirling engine for space power generation is established based on SAGE software, and six parameters, such as the hot-end temperature, cold-end temperature, charging pressure, regenerator’s porosity, wire diameter, and displacer phase angles are selected to explore the effects of different heat exchanger structures （fiber-tubular, screen-tubular, fiber-fin, screen-fin） and thermodynamic parameters on the output performance of the free-piston Stirling engine. The investigation compares the performance of the woven screen matrix/random fiber matrix structure regenerator with that of the fin heater/tubular heater in terms of the thermodynamic parameters, the effects of different heat exchanger structures, and input parameters on the free-piston Stirling engine output performance. The results indicate that the output power and thermal-to-power efficiency of the free-piston Stirling engine increase with the increase of the hot end temperature, and increase and then decrease with the rise of the wire diameter and porosity. The regenerator porosity significantly impacts the output power and thermal-to-power efficiency, and the maximum output power and thermal-to-power efficiency are 15.38 kW and 32.48%, respectively, at a porosity of 0.9. Among the different heat exchanger structures, the maximum values of the thermal-to-power efficiency are 37.04% and 36.23% for the fiber-tubular and screen-tubular structures, respectively, and the tubular heater structures can achieve higher thermal-to-power efficiencies compared to the fin heater structures for different variations of the input parameters. Additionally, the maximum output power for fiber-fin and screen-fin structures reaches 20.25 kW and 20.73 kW, respectively, and the fin heater structure demonstrates superior thermal performance. In conclusion, this paper not only provides a comprehensive analysis of the influence of different heat exchanger structures on output performance but also explores the trends of output power and thermal-to-power efficiency under different thermodynamic parameters. This research contributes a theoretical basis for the performance optimization of free-piston Stirling engines for space applications.