Enzymatic polymerization of aniline was first performed in a perfluorooctanesulfonate acid potassium salt, CF₃(CF₂)₇SO₃K, abbreviated to PFOS, template system with Aspergillus laccase/O₂ as catalyst and oxidant and then functionalized cotton, possessing special electro-optical properties and variable wettability, was prepared by in situ polymerization of aniline under optimal conditions. The chemical structure and composition characterizations of the cotton fabric were carried out using corresponding characterization techniques, which indicated that, in the process of in situ polymerization, the hydroxyl groups in cotton cellulose, to a certain extent, could also be involved in the reaction and confirmed that the hydrophobicity of treated cotton (with a maximal contact angle of approximately 124°) was a result of the synergetic effect of low surface energy of PFOS and the coexistence of micro/nano structures on the cotton surface. The results of cyclic voltammetry, fiber resistance testing, and thermal analyses proved that the electro-optical properties and thermal stability of cotton fabric were drastically enhanced by PFOS-doped PANI. Utilizing the doping/dedoping process of PANI, the wettability of treated cotton underwent a reversible change from hydrophilic to hydrophobic. Color tests and zeta potential measurements served as auxiliary evidence to explain the mechanism of the wettability switch of the functionalized cotton. The stability of PFOS-doped PANI on the cotton surface was evaluated by a washing fastness test, which showed that the contact angle of the treated cotton could still reach 94.5° after 25 cycles of water washing.