To investigate the effect of rotor design configuration on hemodynamic features, hemocompatibility and dynamic balance of blood pumps. Computational fluid dynamics was employed to investigate the effects of rotor type (closed impeller, semi‐open impeller), clearance height and back vanes on blood pump performance. In particular, the Eulerian hemolysis model based on a power‐law function and the Lagrangian thrombus model with integrated stress accumulation and residence time were applied to evaluate the hemocompatibility of the blood pump. This study shows that compared to the closed impeller, the semi‐open impeller can improve hemolysis at a slight sacrifice in head pressure, but increase the risk of thrombogenic potential and disrupt rotor dynamic balance. For the semi‐open impeller, the pressure head, hemolysis, and axial thrust of the blood pump decrease with increasing front clearance, and the risk of thrombosis increases first and then decreases with increasing front clearance. Variations in back clearance have little effect on pressure head, but larger on back clearance, worsens hemolysis, thrombogenic potential and rotor dynamic balance. The employment of back vanes has little effect on the pressure head. All back vanes configurations have an increased risk of hemolysis in the blood pump but are beneficial for the improvement of the rotor dynamic balance of the blood pump. Reasonable back vanes configuration (higher height, wider width, longer length and more number) decreases the flow separation, increases the velocity of blood in the back clearance, and reduces the risk of blood pooling and thrombosis. It was also found that hemolysis index (HI) was highly negatively correlated with pressure difference between the top and back clearances (r = −.87), and thrombogenic potential was positively correlated with pressure difference between the top and back clearances (r = .71). This study found that rotor type, clearance height, and back vanes significantly affect the hydraulic performance, hemocompatibility and rotor dynamic balance of centrifugal blood pumps through secondary flow. These parameters should be carefully selected when designing and optimizing centrifugal blood pumps for improving the blood pump clinical outcomes.