According to the structural design scheme for the main tube of a tracking system fixed on a moving vehicle, the Finite Element Method (FEA) model is established with the software Ansys Workbench. The first ten natural frequency and the distributions of the structural strength are obtained. And it is concluded that the relative position of the primary and secondary mirror is the interesting factor. Therefore, three parameters are defined to describe the variance of the relative position. Finally, the transient responses of three parameters due to the load impact are analyzed. The analysis results are provided for the dynamic optimal design and the vibration analysis of the whole tracking system.