In the structural calculation of pumping station project, the spatial three-dimensional finite element software compared with the conventional method can reflect more actual working conditions of pumping station engineering, This paper takes the project of Jinhekou drainage and irrigation station in Hexian County as an example, the MARC finite element software was used to establish a three-dimensional structure model, and the stress and displacement were reseaidned and analyzed. The results show that the structural strength of most components of the pump station does not meet the requirements of the specification, and it is urgent to reinforce the pump station.