Perpendicularity outoftolerance of gantry milling boring machining center of lathe bedX axis and vertical beams Yaxis is the main aspect of perpendicularity error. To analyze the causes and find, beam gravity is one of the important reasons which caused the error. The finite element analysis (FEA) technology was used to research that 11 positions gravity deformation of the beam. The corresponding deformation values of up and down guide rail base plane and location were gotten. As a result, the shape of base level and location which should be processed is obtained. Thus, the existing machining process of beams was improved. Through the test finding that after compensation process, the straightness error of the existing process was eliminated basically, and perpendicularity error was reduced by 85%. It is illustrating that the process improvement method for the problem solving has feasibility and effectiveness.