Abstract: The continuous wave radar is the main tracking equipment for trajectory observing at present. Estimation and calibration of system errors have important significance. In this paper, according to that the trajectory equation in free flyiny can be obtained accurately, we build a nonlinear model for estimating system error of free flying trajectory by use of trajectory equation and give the relevant algorithm. Specially, by use of this method, we can give high precision estimation of system error only using the tracking data of a set of MISTRAM.