According to model analysis of gilling machine’s hauling box, this paper presents the research on the complex structure’s model analysis. Before the analysis of box, the paper inducted general analysis process, then the box was divided into 8 modules, advanced function MPC and super-element were used to process connection among these modules, the processed model was analyzed by finite-element software Nastran. The result from Nastran include natural frequencies and mode shapes, which are similar to actual work condition. It can be concluded that the process for complex structure is accurate. The result is useful to find the reason of box vibration, and it is also used for optimization design.