In this paper, the design of the GPS and Baro-Altimeter integrated navigation system was presented and the mathematical models were founded for the system. Unified the positioning principle of GPS, observation equation of GPS and Baro-Altimeter integrated navigation localization system as well as the resolving method of the observation equation was given. Using Federal Kalman filter algorithm, achieved the data fusion of GPS and Baro-Altimeter. at last, a lot of experiments and emulators were made to exam the integrated navigation system, as the result showed, if the information offered by the Baro-Altimeter was accuracy, it can be ensured the aircraft precision approach and the capacity of the terminal navigation, and improved safety and reliability of the aircraft. This integrated navigation solution has the benefits of simple in principle and easy to achieve.