With the k-ε renormalization group turbulence model, the drag reduction mechanism of three- dimensional spherical crown microstructure of different protruding heights distributing on the groove surface was studied in this paper. These spherical crown microstructures were divided into two categories according to the positive and negative of protruding height. The positive spherical crown micro-structures can destroy a large number of vortexes on the groove surface, which increases relative friction between water flow and the groove surface. With decreasing the vertical height of the spherical crown microstructure, the number of rupture vortexes gradually decreases. Due to the still water area causes by the blocking effect of the spherical crown microstructure, it was found that the shear stress on the groove surface can be reduced, which can form the entire drag reduction state. In another case, the spherical crown microstructures protrude in the negative direction, vortexes can be generated inside the spherical crown, it was found that these vortexes can effectively reduce the resistance in terms of pressure and friction. In a small volume, it was shown that the surface drag reduction rate of spherical crown microstructures protrudes in negative directions can be the same as high as 24.8%.