The modernization of pumping station management plays an important part of modern management of water conservancy projects. The evaluation of pumping station management modernization provides a scientific basis for the decision-making of pumping station management reform and innovation. In order to scientifically evaluate the modernization of pumping station management, and solve the problem of incompatibility among evaluation indexes, a modernized evaluation index system of pumping station management composed of five first-level evaluation indexes and 24 second-level evaluation indexes. The entropy weight method and the expert weighting method were used to get the comprehensive weight. A modern matter-element evaluation model of pumping station management was established and applied to the Fenghuangjing pumping station. The results showed that the matter-element analysis method can effectively evaluate the modern management level of pumping station, which is consistent with the actual situation. The modern management level of the pumping station is excellent, but the management of water ecological management and water resources information management should be strengthened. In particular, water conservancy information resources management and soil erosion control need to strengthen modernization.