The motions of port valves are a primary aspect to consider in achieving superior reliability and performance of a diaphragm pump, and it is necessary to perform detailed analyses to stabilize the motions of port valves. A transient 3D fluid-structure interaction (FSI) model was proposed to simulate a complete working process of a diaphragm pump and the motions of port valves. The dynamic mesh technique was used, and the deformation of the diaphragm was considered. Detailed descriptions of the FSI model creation development and the simulation methodology for the diaphragm pump were provided. Based on the FSI model, the influences of the back pressure and pump speed on the dynamic characteristics of port valves were analyzed, and the flow rate of the prototype was tested under different conditions on a test rig. The simulation results indicate that an increase in the back pressure and pump speed can lead to a reduction in the flow rate. The motions of the port valves are dependent on the back pressure and pump speed, and the deformation of the diaphragm is only dependent on the back pressure. The opening lag angles of the port valves increase significantly as the back pressure increases, but they are independent of the pump speed. In addition, the opening velocities of the port valves increase with increasing back pressure and pump speed. Finally, the simulation results also show agreement with the experimental data, and the FSI simulation method can predict the dynamic characteristics of port valves in a diaphragm pump. INDEX TERMS Diaphragm pump, port valves, dynamic characteristics, fluid structure interaction (FSI), dynamic mesh technique.