Abstract: In view of reducing the micro-vibration impact on the sensitive payloads of a spacecraft, the micro-vibration suppression effect of rubber isolators on pulse tube cryocooler inside the payload was studied in this article. Firstly, the characteristics of the micro-vibration source of the cryocooler was analyzed. Secondly, based on the vibration isolation requirements for sensitive payloads, a passive isolation scheme was determined, and the performance of the rubber isolator were verified through quasi-static and sweep frequency testings. Mechanical bearing capacity was tested on the isolation system under active section launching condition, and micro-vibration attenuation was examined at room temperature. Finally, rubber isolators that meet the requirements for both the active section and the working section in orbit were selected. The results show that the cryocooler equipped with vibration isolation systems can withstand the impact from active section launch shock with high structural stability. The micro-vibration attenuation can be 34.12 dB, meeting the expected requirement of >24 dB. The research may provide a technical reference for the micro-vibration suppression for cryocooler and optimize its overall design in the future.