For the problem of uncertain noise leads to the accuracy decrease of the filter performance, a GPS/INS integrated navigation algorithm based on multi-sensor uncertain effects is presented. The state and measurement equations of the navigation system are established, and the equivalent measurements and the corresponding error matrix are estimated by using the proposed method. The results are submitted into the system model for filtering, and the exact location of the vehicle is obtained. The experiment in GPS/INS navigation system shows that, the fusion result with uncertainty effect is better than the fusion result with independent noise due to the consideration of correlated noise and uncertain effects, and also verifies the effectiveness and practicality of the proposed algorithm.