Abstract: Vibration disturbances generated by mechanical cryocooler are critical issue in practical application,because they will affect the resolution and position accuracy of the space exploration instruments.To reduce the disturbances generated by Stirling Cryocooler in application,we introduce the adaptive active vibration control algorithm into the system.This paper has analyzed the principle,advantages and disadvantages of current method.Its stability and convergence would be severely restricted,for it relies on the transfer function of the actuator.Base on modified filtered-x fast affine projection algorithm,the adaptive control system which consists of controller and vibration sensor is proposed.With compared to the conventional method,it can get rid of the effect of transfer function,and its stability,convergence and robustness are better.