The Stirling refrigerator has been widely used for the cooling of the infrared and cryo-sensor, The Stirling refrigerator has the clearance in the compressor and cold finger. The cooling capacity of the Stirling refrigerator comes from the relation of the pressure in the expansion space and motion of displacer. In the radial clearance of the cold finger, the parasitic dynamic losses from the leakage flow and shuttle heat losses are inevitably occurred. Therefore, to get the maximum performance of the refrigerator, the radial clearance should be optimized. In this study, the influences of the radial clearance on the performance were investigated by numerical simulation. The results show the effects of the radial clearance, operating frequency and the stroke of the displacer on the cooling performance of the Stirling refrigerator (the enthalpy flow through the regenerator and clearance, the shuttle loss).