An approach for real-time detecting and isolateing GPS fault in pseudo range and pseudo range rate was presented for tightly integrated missile-borne navigation system composed of SINS and GPS. First, the tightly integration algorithm which takes GPS pseudo range and pseudo range rate directly as measurements was deduced based on SINS navigation error model and Kalman filtering theory. On the basis, a GPS fault detection method based on residual chi-square test and a GPS fault isolation method based on Chebyshev theorem ware designed through analyzing statistical characteristics of the filter residual. Simulation results showed that the proposed algorithm can further improve the system in anti-interference ability and thus guarantee navigation accuracy effectively when-fault occurs to information from one or more satellites occur fault.