The invention provides a medical waste pollution treatment system, comprising a screening machine, a crusher, a grinder, a cyclone furnace, a cold quenching pool and a sediment pool which are connected in turn; the screening machine is used to sort medical waste, and the crusher is used to crush the sorted medical waste; the grinder is used to grind the crushed medical waste and raw coal which are mixed at the mass ratio of 1:2; the cyclone furnace is used to burn the mixture ground by the grinder to molten state, then the molten mixture is conveyed to the cold quenching pool through pipelines for cold quenching, and the sediment pool is used to precipitate and filter the product after cold quenching. The medical waste pollution treatment system provided by the invention can solve the environment pollution problem caused by heavy metal-containing sludge in the medical waste.