2024 aluminum alloy is widely used because of its high strength, low density, strong corrosion resistance, good heat resistance, light material and other excellent properties. However, in the ultra-precision machining process, its crystal structure often changes due to tool extrusion, resulting in changes in its physical properties such as plasticity and adhesion, which seriously affects the machining quality and tool wear. At present, aluminum alloy cutting is mainly carried out by cemented carbide tools. In this paper, the simulation experiment of WC tool cutting 2024 aluminum alloy is carried out based on MD (molecular dynamics) simulation method. The CNA (common neighbor analysis), DXA (dislocation analysis) and Coordination (coordination analysis) methods are used to study the tool diffusion wear mechanism and the influence of crystal evolution on tool diffusion wear based on the change of cutting parameters from the microscopic point of view. The results show that diffusion wear is the main factor causing WC tool wear. The defect evolution of the workpiece during the cutting process will directly affect the cutting force and cutting temperature, thus affecting the diffusion wear of the tool. The cutting speed, cutting width, cutting depth and tool clearance angle have a regular effect on the defect evolution of workpiece atoms and the order degree of tool atoms in the cutting process. At the same time, this paper verifies the correctness of the simulation results through milling experiments. The research results based on molecular dynamics simulation are reliable, which can greatly reduce the test cost and improve the efficiency of scientific research. It provides a reference for further improving the surface quality of ultra-precision cutting of aluminum-based alloy materials and reducing tool wear.