The invention provides a method for preparing fluorinated graphene through a microwave hydrothermal method. The fluorinated graphene is prepared by employing the microwave hydrothermal method and is rapidly heated by utilizing the change of the electric field and magnetic field in the space, the low-temperature (150-200 DEG C) temperature is realized, the reaction time (30-60 minutes) is greatly shortened, the energy consumption is reduced, and the preparation efficiency is improved. The adopted preparation method does not have temperature gradient in the reaction process, a hysteresis effect is avoided, and the reaction process is easy to control and fewer in influence factors; and the prepared fluorinated graphene is uniform in fluorine doping and high in experimental repeatability. The process conditions such as raw material ratio, reaction temperature and reaction time are adjusted, and the fluorinated graphene of different fluorine contents can be prepared. The prepared fluorinated graphene is high in yield, and the yield is up to 90-95 percent. The preparation method is easily popularized and applied.