For such complex rotating machinery as hydraulic turbine, the hydraulic operation characteristics of the hydraulic turbine unit are significantly impacted by the short blade of the runner used as the splitter blade. To find the optimum position of the short blade, the study object is the 1000 MW hydraulic turbine, selects three circumferential offset positions of the short blade for numerical simulation calculation, obtains the runner flow pattern at different offsets, and explores the impact on the short blade offset on the vortex and pressure pulsation in the runner. The results show that the counterclockwise offset of the short blade will improve the flow pattern of the runner, reduce the scale of vortex in the runner and enhance the efficiency of the hydraulic turbine. The counterclockwise offset will increase the interference while decreasing the pressure pulsation in the vaneless region, at the runner's inlet, and downstream of the short blade. When the offset d=0.6, the peak-valley difference of pressure fluctuation in the vaneless zone is the smallest, accounting for only 1.38 % of the rated head. The main frequency of the vaneless zone gradually changes from 15fn to 30fn, and the main frequency of the runner inlet and the short blade downstream is 24fn. Due to the different weakening effects of short blades on the interference, low-frequency pulsation components of 4fn and 8fn appear.