During the operation of a Pelton turbine, the centerline of the nozzle jet may deviate from the bucket pitch circle due to the low installation and maintenance accuracy, which will reduce the operating efficiency and the stability of the turbine and even cause severe vibrations and damages. Based on the VOF (Volume of Fluid) two-phase flow model and the SST k-ω turbulence model, the flow characteristics of a Pelton turbine were simulated with the nozzle jet deviating from the bucket pitch circle. The pressure pulsation inside the bucket and the force distribution of the runner were obtained, the turbine oscillation and efficiency were measured before and after the jet deviation, and the effects of the radial and axial deviations on the stability and efficiency of the Pelton turbine were analyzed. The results show that both the radial and axial deviations of the jet cause a significant increase in the axial force and the pressure pulsation amplitude of the turbine; the radial and tangential forces on the runner are slightly reduced; the maximum axial force on the runner is increased by 4 times and 2 times, respectively, after the axial and radial deviations within the maximum value allowed by the industry standard; and the efficiency of the turbine is reduced by 0.4% and 0.3%, respectively. The maximum relative amplitude of pressure pulsation in the radial offset case appears in the center of the bucket blade, while the axial offset case causes uneven pressure distribution on both sides of the diverter blade, uneven force on the bucket blade of the runner, and fatigue damage. By comparing the operation of the runner under the two offset cases, we can find that the axial offset of the jet has a greater impact on the stability of the runner than the radial offset, and the unit is more prone to vibration, increasing the risk of the unit lifting.