For the problem of the master/slave inertial navigation system(INS) online calibration error equation multifaceted impacted by flexure, a comprehensive error compensation method is proposed. The auto regressive model(AR) model based on maximum likelihood estimation and Akaike information criterion(AIC) order is used to determine the flexure modeling parameter at first. Then for the dynamic lever arm effect problem caused by flexure, the mechanism modeling method is used to establish a dynamic arm and flexure angle between the relational models. The comprehensive error compensation method on the basis of the flexure and the dynamic lever arm is deduced. Finally, the method is applied to master/slave INS calibration filter design. The simulation results show the effectiveness of the proposed comprehensive compensation method.