In order to satisfy the requirement of power system for deep-space exploration, key issues for designing free piston Stirling engine were analyzed. With the thermodynamic and kinetic coupling designing ideas, we designed a set of free piston Stirling engine whose output power is 100W at operating pressures 8bar, hot space temperatures 700K, and cold space temperatures 300K, operated at 50Hz with helium as working media. Fin structure was selected for heater and cooler to increase heat exchange area and improve heat transfer performance. Temperature distribution of the engine was analyzed. The calculated results indicated that hot space and cold space temperature kept constant value, and the regenerator had a higher temperature gradient. Clearance seal technology was used in piston sealing. Influence of temperature distribution on the deformation of the clearance seal structure was calculated, and the simulation results show that the maximum radial thermal deformation was 90μm at the hot end of the displacer, and the maximum axial thermal deformation was 149μm at the hot end of the regenerator shell.