According to the limit working conditions of the gantry milling machine column, this paper adopts Parametric Design Language APDL to set up finite element model and make finite element analysis. Based on the analysis, the topology optimization method of column structure is proposed, and the optimal design method is established to minimize the weight. The finite element analysis is made again to analyze the rearranged column structure. Compared with the design made through experience, optimally designed column can reduce 10% weight. And the critical displacement and maximum stress are not affected.