Abstract: Hydropower development is in urgent demand in Southwest China, and the Pelton turbine has become the core equipment due to its adaptability to high-head operating. In this paper, the model Pelton turbine of Subagu hydropower plant in Sichuan Province is chosen, and three-dimensional unsteady multi-phase flow simulation has been conducted based on model tests to analyze the effect of operating water head on the turbine’s hydraulic performance and internal flow characteristics. Model test results show that the turbine maximum efficiency is about 90.17% within the range of 0.94 H0~0.98 H0 head at the rated nozzle opening. Predicted results show that at the rated opening, the injector efficiency is nearly unchanged with the variation of the head. The turbine hydraulic efficiency first increases and then decreases as the head rises, reaching a peak of 91.24% at 0.94 H0, with a relative error of 1.2% compared with the model test. Within the range of 0.88 H0 to 1.25 H0, the turbine hydraulic efficiency fluctuates between 89.75% and 91.24%, which is primarily governed by variations in runner hydraulic efficiency. According to the comparison of the unsteady flow process at three different head conditions, the jet morphology remains basically consistent with different heads, whereas the water sheet flow pattern on the bucket surface changes. Water sheet leakage occurs at the bucket cutout, and the leakage volume increases with the rise of the head. The leakage at the bucket cutout is the primary flow-induced cause of aggravated hydraulic loss. This research provides an important reference for the hydraulic design of high-head Pelton turbines.