Whether to synchronize high-precision for their clocks inter aircraft cooperation in aviation swarm is one of key technologies in imposing restriction on the effective cooperation among aircraft. And a high-precision clock self synchronization algorithm is proposed. Taking RTT synchronization as the principle, a synchronization error solution equation containing relative radial motion velocity variables is derived by analyzing the impact of relative motion of aviation nodes on synchronization accuracy. On this basis, a pseudo code acquisition algorithm is proposed based on segmented correlation and frequency domain processing, and the algorithm has a comparative strong ability in anti-Doppler frequency shift. The simulation experiments show that this algorithm can effectively eliminate clock synchronization errors caused by relative motion with the signal time of arrival (TOA) estimation and the Doppler frequency offset estimation being high in accuracy, and low in computational complexity.