The paper introduces tolerance analysis technology and its basic theory. The research uses tolerance analysis software VSA to study the process of civil aircraft pylon assembly. The process one: connecting rod is installed at last. The process two: diagonal bracing rod is installed at last. Comparing process one with process two, the following results can be obtained. Both of two assembly programs are required to set the process compensation. According to the weights of influencing factors, some measures should be applied on the greatest effects for control target. Therefore, improve the design of connecting rod structure to make upper and lower nodal hole position in a certain range to meet the coordination requirements of pylon assembly.