When a missile runs under the complex situation such as high dynamic flying, receiver signal being blocked and so on, the GNSS receiver sometimes gets less than four satellites. For the loosely coupled system, the navigation accuracy will decrease over time. In this paper ,tightly coupled integrated navigation system which is based on pseudo range and pseudo range rate dynamically adjusts the dimension of the system according to the number of visible satellites, in order to achieve seamlessly navigation; a multiple step optimum precision factor satellite selection algorithm is proposed, an error compensation method which is based on the state transition is designed and implemented. Experiments show that when the number of visible satellites changes, tightly coupled system can seamlessly switch, when more than four satellites are received, the multiple step optimum precision factor selection algorithm can provide a combination of high precision satellites, by applying the error compensation method to calibrating the system, high-precision navigation can be achieved.