Surface grafted polymer brush is an effective method of improving surface physicochemical property and preventing adsorption of biomacromolecules including protein as well as other fouling organisms. Fluoropolymer is an ideal constituent forming amphiphilic polymer brush due to its strong hydrophobicity, low surface energy and low surface adhesive force. Forming method, category and antifouling mechanism of fluorine-containing amphiphilic polymer brush were overviewed, latest research results of this coating in anti-protein, germ, alga and other fouling organisms were introduced emphatically. Effects of such factors as chemical composition, surface reconstruction and elasticity modulus of the brush on microphase separation behavior and antifouling property were analyzed in detail. Ratio of hydrophilic and hydrophobic constituents had certain effects on phase separation behavior of the coating. Phase separation structures in different size and morphology might take shape by changing ratio of hydrophilic and hydrophobic constituents, antifouling property of the coating was further affected. Connection mode of hydrophilic and hydrophobic constituents might affect reconstruction behavior of the coating surface, transform the hydrophilic and hydrophobic constituents, and control antifouling behavior of the coating surface. Antifouling mechanism of the fluorine-containing amphiphilic polymer brush was preliminarily revealed from the aspect of molecular design. Finally, it was pointed out that developing multifunctional fluorine-containing amphiphilic polymer brush featuring in several synergistic antifouling mechanisms would be major development trend of amphiphilic polymer coating in the future.