The jet pump is one of the most popular types of fluid machinery in agriculture, industry and environmental engineering and many other fields. However, its internal flow structure is complex, showing obvious unsteady characteristics. The effect of throat diameter size on jet pump performance and energy property was investigated in this study based on numerical calculation and test verification, in order to improve the performance and internal flow field stability of jet pump. Five models with different throat diameters were obtained by adjusting the assembly structure and simulated by the computational fluid dynamics software to solve the Navier–Stokes equations for three-dimensional steady flow. The accuracy of numerical methods was verified by comparison with the experimental results. The compact jet pump performance under different throat diameters was then compared and analysed. The backflow at effuser outlet of different throat diameters causes the changes of vortex structure inside the injector rear chamber. The vortex diffuses downstream to the impeller inlet, making the flow structure of the impeller inlet show obvious circumferential inhomogeneity. This forms different vortex structures at different impeller flow channels, changing the distribution of entropy production within the impeller, ultimately leading to a decrease of pump efficiency. Therefore, this study found that selecting a reasonable throat diameter of the injector can improve the performance of the jet pump impeller, and thus improve the overall efficiency of the system. For the research object in this paper, the recommended range of throat diameter of injector is 16 mm–17 mm. This finding could provide useful insights for the improvement of the hydraulic performance and operational stability of compact jet pumps.