Non-axisymmetric flow structure in a mixed flow pump could lead to series of serve adverse phenomena, such as large hydraulic loss, strong pressure fluctuations and vibrations even under the design point condition. In this paper, numerical investigations have been carried out on the effect of non-axisymmetric flow in a mixed flow pump using a modified shear stress transfer k-ω partially averaged Navier-Stokes model. The numerically predicted pump head agreed well with the measured results. The flow analysis indicates that the non-axisymmetric geometry of pump casing causes great energy loss, and even severely complicated flow structures upstream the pump casing. It is noted that high pressure gradient on impeller blade surfaces and pump casing walls results in large radial force acting on pump shaft. To alleviate the adverse phenomena due to non-axisymmetric flow in the pump, the modifications of diffuser vanes and pump casing were carried out. The results show that suitable applications of a thicker diffuser vane on the pressure side and extended diffuser vane may contribute to reducing the radial force. Based on these results, an improved model of the mixed flow pump has been proposed, which has the lowest radial force as well as relative better hydraulic performance.