Fluorinated graphene quantum dots (FGQDs) have distinctive charge distribution in structure and unique chemical bonds in composition, corresponding to novel performance different from common quantum dots. However, their synthesis is a challenge due to chemically inert CF bonds and hydrophobic nature, and the fluorine influence on FGQDs remains scarce and to be studied. Herein, we first design a gradient fluorine-sacrificing strategy to synthesize FGQDs with controllable sizes and tunable fluorine contents from bulk fluorinated graphite. It is found that although fluorine atom is the second-smallest in periodic table, it not only greatly affects the size formation process, but also endows FGQDs with pH-independent luminescence without any additional surface passivation. And it is for the first time to experimentally observed that point defects in FGQDs induced by fluorine can greatly increase paramagnetism, which is 5 times higher than unfluorinated ones. Moreover, cytotoxicity experiments clearly reveal FGQDs show good biocompatibility, and it is the chemical surface rather than size that influences the cell viability. This work realizes fine control over both structure and chemistry of FGQDs, and thus allows a better insight into the fluorine effects on formation and performance of graphene quantum dots.