Ground based augmentation system (GBAS) can strongly support aircraft’s precise approach landing, and integrity monitoring is not only the difficulty of the system realization but also the key point to safeguard the flight. In order to ensure the reliability of the differential correction from the GBAS ground station, the B value calculation and fault monitoring process in the multiple reference consistency check (MRCC) are used to eliminate the receiver channel which generates a lot of error in the correction. The principle and method of MRCC algorithm are analyzed in this paper, the problem of pseudo range and carrier phase B values are both more than threshold and the maximum value is not in the same channel are founded in the MRCC fault monitoring process. An improved algorithm of MRCC fault monitoring process is proposed for this problem, then the existing and improved MRCC fault detection algorithms are compared in the experiment. The results indicate that the improved algorithm can effectively solve the current problems in the hierarchical process of the inconsistency caused by the pseudo range and carrier phase.