For improving the efficiency of trajectory accuracy’s influencing factors analysis, the method of two-steps variance analysis was presented. Based on the judging criterion of trajectory accuracy, firstly, the important influencing factors of trajectory accuracy were found by the method of one-way ANOVA. Then, considering the interaction between each factor, the variance analysis method based on orthogonal test was used to confirm the main error parameter of trajectory accuracy. The result shows that the method could select the significant influencing factors of trajectory accuracy efficiently under the assumption of ensuring the result’s dependability. According to the significant influencing factors, the optimal level collocation of factors could be confirmed in order to plan the test more efficiently. The method could also decrease the frequency of simulation test and have some guiding significance for the parameter optimization.