The invention discloses a mineral repair agent which is prepared from fluoro-based apatite and kaolin in a mixing manner, wherein the weight ratio of the fluoro-based apatite to the kaolin is (95 to 5)-(90 to 10). The invention also discloses a preparation method of the mineral repair agent and application of the mineral repair agent in water body lead pollution repair. The mineral repair agent disclosed by the invention has the characteristics of being low in cost, high in treatment speed and free of secondary pollution. For high-concentration lead-containing waste water having the high lead concentration, the mineral repair agent can remove 20g/L of free lead in water within half an hour according to the flow.