As a functional outermost structure surrounding cyanobacteria cells, the surface coats play an important role in morphological adaption, which further influence the dominance and persistence of cyanobacterial blooms in freshwaters. In recent years, there have been extensive studies on the characteristics, structures and components, regulating factors, and industrial applications of cyanobacterial surface coats. The biological function of cyanobacterial surface coats and their molecular regulation mechanisms have still not been clearly understood. In this paper, with the development of analytical technology, we summarized the production, biological functions and especially the molecular response mechanisms of cyanobacterial surface coats in freshwaters. We reviewed the biological functions of surface coats in the following four aspects: 1) serving as a protective barrier against environmental stress, 2) participating in mass transport and storage, 3) motivating the movement, 4) promoting the aggregation and cyanobacterial blooms in freshwaters. In addition, we analyzed current molecular biological research advances on the synthesis of cyanobacterial surface coats. We also discussed the molecular regulation mechanisms of cyanobacteria in response to external environments via surface coats. Finally, we proposed future focus on the cyanobacterial surface coats.