The integrated navigation system can improve the navigation accuracy utilizing the redundant information. The Extended Kalman Filter (EKF) is commonly used in the integrated navigation system. It usually takes only one-order of Taylor expansion and needs to calculate the Jacobian matrix, which will affect the accuracy and numerical stability of the system significantly. Thus in this paper the application of Square-Root Cubature Kalman Filter(SCKF) method was proposed to solve the above problems in the SINS/CNS integrated navigation system. The simulation results show that the position, velocity and attitude errors are reduced effectively compared with the EKF method. The SCKF method is more suitable for the state estimation problems in integrated navigation system.