Waterjet propulsion has many advantages when operating at high-speed conditions. As a special way of navigation, it is mostly used in high-speed ships and shallow draft ships. In this paper, a mixed-flow waterjet pump was taken as the research object. For the two cases of non-uniform inflow and uniform inflow, a modified RANS/LES method was adopted for unsteady calculation of the whole channel, aiming at investigating the influence mechanism of the non-uniform inflow on the energy performance and pressure pulsation characteristics of the waterjet pump. The hydrodynamic characteristics of the waterjet pump were comprehensively analyzed such as head, efficiency, axial-force, internal flow and pressure pulsation. It is found that the non-uniform inflow will reduce the external characteristics of the waterjet pump and lead to the huge fluctuation of energy performance with time. Low-speed swirls occur locally in the intake duct for non-uniform inflow, in which condition the vorticity is much higher than that for uniform inflow. In terms of the low-speed area, PRey and Ptur, the values under non-uniform inflow condition are generally larger than those under uniform flow condition when in the impeller and guide vane zone. The dominant frequencies of pressure pulsation are, respectively, fn, 7fn and 4fn in the intake duct, impeller and diffuser, which are almost consitent for the two cases. However, the frequency features are more diverse, and the amplitudes corresponding to the same frequencies are more intense for non-uniform inflow.