The accuracy of SINS/GPS integrated navigation system will decline when there is a large initial misalignment angle. To solve the problem, a navigation algorithm based on center difference Kalman filter was proposed. For the sake of the synchronization of the attitude parameters and other parameters in the process of Sigma point sampling, Euler angle was chosen as attitude parameter. In order to avoid high computation and the complexity of transcendental equation solving, Euler angles were switched to quaternions when propagate following the system equation. The simulation results show that the proposed algorithm has a higher convergence speed and accuracy than the additive quaternion algorithm.