Physical processes such as vertical turbulence, temperature, and light are key factors affecting vertical distribution and algae growth. Based on the radiation, water depth, water temperature and water attenuation, sensitivity studies were conducted using algae growth-diffusion model to explore the mechanism of physical processes affecting the vertical distribution of sinking algae. The results showed that the vertical distributions of sinking algae were affected by vertical turbulence, temperature and light. Water temperature was the limiting factor for the generation of the Subsurface Chlorophyll Maxinmum (SCMax) or Subsurface Chlorophyll Minimum (SCMin). When the water temperature was higher than the threshold, with the increase of the depth, the key to the generation of SCMax was that the too much light could inhibit the growth of algae, and the weak light could limit the growth of algae. The entrainment of vertical turbulence was the key process of weakening SCMax intensity. This study favored to clarify the mechanism of cyanobacterial bloom and strengthen the restoration for aquatic ecosystem.