Hydropower is a major source of renewable, noncarbon-based electrical energy. Although hydropower has many environmental advantages, hydropower dams alter the natural ecohydrological conditions of the rivers and cause significant ecological impact, especially for fish that live in or migrate through impounded river systems. Injury and mortality of fish that pass through hydraulic turbines and other downstream passage routes can result from several mechanisms, such as rapid and extreme pressure changes, shear stress, strike, cavitation, and grinding. For example, a large or fast pressure drop can lead to internal bleeding of fish, rupture of the swim bladder or vapor bubbles in eyes, which will result in direct mortality and reduces the ability to escape predators in the tailrace. Shear stress can causes fish scales flake, muscle tissue tearing, bruising, and even the fish body are cut off. So understanding the biological responses of fish to the conditions of hydraulic turbine is important for designing advanced fish-friendly turbines. Since the injury of fish may be caused by a combination of multiple damage mechanisms, it is necessary to identify primary and secondary damage mechanisms by research. In this paper, the computational fluid dynamic analyze method was adopted to simulate the three dimensional turbulent flow in an francis turbine. The simulation was conducted at different discharge conditions of maximum, rated and minimum head. The rated head of the turbine Hr is 106 m, the maximum head Hmax is 120 m and the minimum head Hmin is 73 m. The whole flow passage of the turbine was discretized by hexahedron structured mesh, and the SST k-ω turbulence model was used in the simulations. Then, the fish friendly threshold for pressure, pressure change rate and shear strain rate were used to analyze the volume size and distribution that may lead to the damage of fish. The ratio of the volume exceeding the fish friendly threshold to the total volume of the runner channel was defined as the fish damage probability. Finally, according to the calculation results, the main and secondary mechanisms of fish damage under different conditions were identified. Meanwhile, the law between the probability of fish injury caused by these mechanisms and the working conditions was further analyzed. From the results it can be seen that the volume which the pressure beyond the threshold in runner is mainly distributed at the outlet of the suction side of the runner blade, and the volume which the pressure change rate beyond the threshold is distributed at the leading and trailing edge of the runner blade. Besides, the volume which the shear strain rate beyond the threshold is distributed near the wall of the crown, band and runner blade. The fish damage probability caused by pressure, shear stress and pressure change rate were defined as P(A), P(B) and P(C) respectively in this paper. Based on the results of this paper, the probability P(A) reaches the maximum value at the condition L1. And the probability P(B) and P(C) reach the maximum value at the rated condition R1. The maximum value of P(A), P(B) and P(C) are 9.1%, 0.823% and 8.31% respectively. By comparing the fish damage probability of pressure, pressure change rate and shear stress under different discharge conditions at the same head, it can be concluded that the minimum pressure and the pressure change rate are the two important factors to prevent fish damage. The shear stress is less important than that of them. Therefore, in the process of designing fish friendly francis turbine runner, the pressure in the runner must be raised as much as possible. Meanwhile, the pressure change rate in runner must also be decreased.