The interaction between sediment particles and turbulent two-phase media inside hydro-turbine under sand containing water flow conditions has a significant impact on the erosion and wear mechanism of the turbine wall. Based on GPU accelerated coupled particle discrete element (DEM) and computational fluid dynamics (CFD) methods to solve the internal particle fluid system of hydro-turbine, the wear characteristics of sediment particle flow in hydro-turbine through DEM-CFD coupling simulation were obtained by using the real shape modeling of sediment particles. The results showed that GPU acceleration can save computational costs. Sediment particles under coarse sand flow were affected by the water flow and moved in a “short spiral” manner in the draft tube at small opening case, while at big opening case, they moved in a “long spiral” manner. The maximum resistance of spherical polyhedral sediment particles at small opening case was 34.78% higher than that of spherical particles. The collision strength of particles on the guide vanes at big opening case was 74.13% higher than that of the stay vanes, indicating that their impact wear was stronger than that of the stay vanes. The average maximum sliding distance of particles on the stay vanes was 21.43% higher than that of the guide vanes, indicating that their shear wear was stronger than that of the guide vanes. The wear of the guide vanes, runner blades and draft tube walls was consistent with the experimental results in the literature and the actual wear of the power plant. It was beneficial to control the operating case of the hydro-turbine during the flood season and operate it at small opening case. The research result can provide theoretical reference for improving the sediment erosion and damage of hydro-turbine.