The research of marine antifouling is mainly conducted from the aspects of chemistry, physics, and biology. In the present work, the movement model of microorganisms along or against the flow direction on the microstructural surface was established. The model of globose algae with a diameter of 5 μm in the near-wall area was simulated by computational fluid dynamics (CFD), and the fluid kinematic characteristics and shear stress distribution over different-sized microstructures and in micropits were compared. Simulation results revealed that the increase of the β value (height to width ratio) was prone to cause vortexes in micropits. In addition, the closer the low-velocity region of the vortex center to the microstructural surface, the more easily the upper fluid of the microstructure slipped in the vortex flow and reduced the microbial attachment. Moreover, the shear stress in the micropit with a height and width of 2 μm was significantly higher than those in others; thus, microbes in this micropit easily fell off.