Pseudorange error is a key factor affecting the positioning accuracy of the BeiDou satellite navigation receiver. A two-stage pseudorange error compensation method based on the pseudorange difference and the adaptive cubature Kalman filter （CKF） for BeiDou navigation receiver is proposed in this paper. Pseudorange error is divided into the self error and the common error. Firstly， the self error is compensated with the pseudorange difference method. Secondly， the measure noise adaptive CKF filter is designed to estimate the state of the receiver moving system in order to compensate the common error. Experimental results show that the the two-stage compensation method is slightly better under static conditions. The two-stage compensation reduces the localization error significantly than the single-stage compensation when the carrier is dynamic， and the adaptive CKF algorithm has better adaptability to noise and interference than the CKF algorithm.