Aiming at the problem that fixed measurement environments cannot establish a fixed base station and thus cannot carry out precise positioning, a differential positioning algorithm for mobile base station based on BeiDou navigation system was proposed, which means achieving high-precise differential positioning while the base station and the rover both moving. Based on the carrier phase measurement, under the condition of dynamic short baseline, the datum were inter-station and inter-satellite double-difference processed, eliminating receiver clock error and other common errors. Based on the linear combination of multifrequency measurement, the observation of the super-wide lane, the wide lane, the middle lane and the narrow lane was obtained, the window-moving average filter was carried out and the ambiguities were fixed by the stepwise ambiguity determination method, that is, along the order from the super-wide lane to the narrow lane to solve the ambiguity. In order to verify the effectiveness of the algorithm, a verification experiment of the external geometric parameter detector based on the BeiDou navigation system was designed to realize the static relative positioning accuracy of millimeter and the RTK relative positioning accuracy of centimeter.