The invention provides a phosphorus-doped graphene quantum dot and an electrochemistry preparing method thereof. According to the preparing method, phosphorus-contained macromolecular organic compounds soluble in water are selected to serve as electrolytes, through controlled potential electrolyzing, phosphorus oxygen bonds are broken, phosphorus atoms are separated from the macromolecular organic compounds to enter the interior of the graphene quantum dot, carbon phosphorus bonds and the phosphorus oxygen bonds are formed, doping is completed, and the phosphorus-doped graphene quantum dot with the higher doping concentration content is prepared; the quantum dot has the good cleaning-up effect on hydroxyl radicals, and through ESR energy spectrum test, the clearing-up rate of the hydroxyl radicals can reach 78.49%; the method is easy and convenient in the operation process, the whole preparing process is conveniently planed as a whole, strong oxidizing acid or strong reducing agents are not used, and certain commercial feasibility is achieved; and graphene precursor which is rich in reserving and friendly to environment is adopted to replace expensive materials of graphite oxide, carbon nano-tubes and the like, and the method is hopefully and widely applied in the biomedical field.