In this study, the weight analysis of the influencing factors of clearance seal leakage of Stirling cryocoolers was conducted based on the concentric annular gap flow theory. Influencing factors, including sealing gap height, length, pressure difference, motor speed, clearance diameter, and piston stroke, were determined. Through an orthogonal test, 32 sets of mathematical models were established, and the leakages of different seal clearances were analyzed based on the numerical simulation method of computational fluid dynamics. The simulation results were processed using variance analysis, and indicated that the clearance thickness exhibited the most significant influence on the leakage of a Stirling refrigerator. Pressure difference, sealing gap length, piston stroke, and motor speed exhibited a lower influence, where as clearance diameter demonstrated a minimal impact on leakage. This study provides a reference for the design of a Stirling cryocooler clearance seal to reduce leakage.