In the normal operation condition, a conventional square-root cubature Kalman filter (SRCKF) gives sufficiently good estimation results. However, if the measurements are not reliable, the SRCKF may give inaccurate results and diverges by time. This study introduces an adaptive SRCKF algorithm with the filter gain correction for the case of measurement malfunctions. By proposing a switching criterion, an optimal filter is selected from the adaptive and conventional SRCKF according to the measurement quality. A subsystem soft fault detection algorithm is built with the filter residual. Utilizing a clear subsystem fault coefficient, the faulty subsystem is isolated as a result of the system reconstruction. In order to improve the performance of the multi-sensor system, a hybrid fusion algorithm is presented based on the adaptive SRCKF. The state and error covariance matrix are also predicted by the priori fusion estimates, and are updated by the predicted and estimated information of subsystems. The proposed algorithms were applied to the vessel dynamic positioning system simulation. They were compared with normal SRCKF and local estimation weighted fusion algorithm. The simulation results show that the presented adaptive SRCKF improves the robustness of subsystem filtering, and the hybrid fusion algorithm has the better performance. The simulation verifies the effectiveness of the proposed algorithms.