In this paper, the large eddy simulation is utilized to simulate the flow field in a mixed-flow pump based on the standard Smagorinsky subgrid scale model, which is combined with the experiments to investigate pressure fluctuations under low flow conditions. The experimental results indicated that the amplitude of fluctuation at the impeller inlet is the highest, and increases with the reduction of the flow rate. The main frequencies of pressure fluctuation at the impeller inlet, impeller outlet, and vane inlet are blades passing frequency, while the main frequency at the vane outlet changes with the flow rate. The results of the simulation showed that the axial plane velocity at impeller inlet undergoes little change under 0.8 Qopt. In case of 0.4 Qopt, however, the flow field at impeller inlet becomes complicated with the axial plane velocity changing significantly. The flow separation is generated at the leading edge of the suction surface at t* = 0.0416 under 0.4 Qopt, which is caused by the increase of the incidence angle and the influence of the tip leakage flow. When the impeller rotates from t* = 0.0416 to t* = 0.1249, the flow separation intensified and the swirling strength of the separation vortex is gradually increased, leading to the reduction of the static pressure, the rise of adverse pressure gradient, and the generation of backflow. The static pressure at the leading edge of the impeller recovers gradually until the backflow is reached. In addition, the flow separation is the main reason for the intensification of the pressure fluctuation.