The performance of a reversible pump turbine with S-shaped characteristics is of great importance to the transition processes such as start-up and load rejection. In order to improve the "S" characteristics of reduced pump-turbine, several MGV (misaligned guide vane) schemes are calculated. The SST (shear stress turbulence) model is added to the N-S (Navier-strokes) governing equation. In order to predict the S-shaped curve accurately and develop a reliable tool for design improvement, the "S" characteristic is investigated in a whole pump-turbine including spiral casing, stay vanes, guide vanes, runner and draft tube. To validate the scheme reasonable, the mesh independent is tested. Comparison of unit discharge and unit speed performance showed that good correspondence is obtained between experimental data and calculated results. The "S shape" of reduced pump-turbine is eliminated with MGV schemes. Based on this, internal flow analysis is carried out adopting six typical MGV schemes at the same working condition. Through the calculation, we find that, first the pressure fluctuation is different between the guide vane and runner among the five MGV schemes, second the pressure fluctuation amplitude of MGV schemes D (4*35 degrees and 16*6 degrees average installed) is smallest, third the main frequency is the blade passing frequency and guide vane passing frequency at vane-less space and head cover, respectively. The conclusion is the "S shape" of pump-turbine can be improved with the average installed scheme.