An on-orbit low spatial frequency error compensation method has been proposed to restrain low spatial frequency error brought by the difference between on ground calibration and on-orbit environment. Firstly, principle points, initial value of focal length and distortion coefficients are calculated during on-ground calibration. Then, focal length is updated by extended Kalman filter based on angle distance error minimization criterion using selected star pairs during on-orbit calibration. Faster convergence rate and better robustness has been validated by simulation. Sky tests data and on-board data proved that the mean value of angle distance error can be decreased by more than 90% and the low spatial frequency error decreased by more than 40%.