Based on the analysis of inter-satellite distance and clock error computation, the error expressions caused by the relative motion between the satellites are deduced, which provides a theoretical basis for relative motion error elimination. An ideal result of relative motion compensation can be obtained by simulating the relative motion error and using Doppler measurements. In the case of Global Navigation Satellite System(GNSS) constellation, the deviation of clock error measurement can be reduced to 0.001 ns with the proposed method, which can vastly guarantee inter-satellite measurement accuracy and time synchronization precision in the future.