Development of efficient technologies to deal with organic pollutants in wastewater is an important issue. Photocatalysis, as a “green chemistry” technology, has attracted much attention in pollutants degradation and efficient visible-light-driven photocatalysts with powerful ability to completely oxidize organic pollutants in contaminated source water are highly desirable. Here, a series of fluorinated Bi2MoO6 crystals with different atomic ratio of F to Bi (RF=0.10, 0.15, 0.20, 0.25, 0.30) were prepared via a solvothermal-calcination process. The effects of F doping on the physicochemical properties of Bi2MoO6 were investigated by physicochemical techniques like XRD, N2 adsorption, SEM, TEM, UV–Vis DRS, FT-IR, XPS, PL and photoelectrochemical measurement. The substitution of F− anions for the host O2− anions induced the lattice shrinkage, a decrease in crystal size and an increase in crystallinity. Moreover, the oxygen vacancies in F-Bi2MoO6 and F− adsorbed over the catalyst surface could withdraw the photoexcited electrons, largely boosting the separation of photoexcited electron–hole pairs. F0.20-Bi2MoO6 displayed significant photocatalytic performance in removal of phenol, bisphenol A, 4-chlorophenol and Rhodamine B dye. ESR and radicals trapping confirmed holes are mainly responsible for the degradation of the target organic pollutants. However, •OH and •O22− could be also involve in photocatalytic reactions. Meanwhile, the more positive potential of VB in F-Bi2MoO6 could promote the oxidation power of the h+ in organic pollutants removal.