In order to study impact analysis for capability of IEEE 1588 clock synchronization system from different flight test networked condition, the method of using the normal distribution curve to depict clock synchronization error is proposed. By analyzing the theory of the precision of IEEE 1588 clock synchronization system, the method of hardware way is decided to measure the error distributing of the clock synchronization system . By the statistic analysis means, impact for capability of IEEE 1588 clock synchronization system from different flight test networked condition is analyzed. The data result indicates that networked topology、network node load and exterior temperature all have same effect on capability of IEEE 1588 clock synchronization system. And network topology changes will affect a large extent IEEE 1588 clock synchronization accuracy. The research results have certain significance to the design and use of airborne network test system.