Stirling cryocoolers are widely used to refrigerate significant facilities in military and aerospace applications. However, under the influences of high-frequency piston motion and thermal environment deterioration, the refrigerating performance of Stirling cryocoolers will worsen inevitably, thus affecting the successful accomplishment of space mission. In this article, a methodology on assessing the performance of space Stirling cryocoolers is proposed, which involves the analysis of the failure mechanism, health indicator construction and remaining useful life prediction of the cryocooler. The potential factors affecting the refrigerating performance are discussed first. In view of these, three health indicators representing the degradation process of cryocoolers are constructed and then a multi-indicator method based on particle filter is proposed for remaining useful life prediction. Finally, the proposed method is validated by a Stirling cryocooler from one retired aircraft, and the results show that the constructed health indicators and remaining useful life prediciton approaches are effective for performance assessment of Stirling cryocooler.