In order to improve the precision of GPS/SINS integrated navigation system further, after introduce the principle of wavelet’s multi-scale analysis, deduce the theoretical variance model of smooth signal during the wavelet’s multi-scale analysis. When this model is applied to GPS’s output information, the experimental results show that this theoretical variance model is basically consistent with the experimental results; then on the basis of the above, put forwards one new method for GPS/SINS integrated system based on the theoretical variance model of GPS output information, and then this new method is validated by the practical static experiment. The experimental results show that when this method is used, the precision of every navigation parameter is improved obviously.