The invention discloses an intelligent classified recovery system of medical waste and a control method of the intelligent classified recovery system. The intelligent classified recovery system of the medical waste comprises a separating wall, a window, a receiving device, an output device, a conveyor belt and a plurality of waste collection devices, wherein the separating wall is used for forming a first chamber and a second chamber, which are isolated from each other; the window penetrates through the separating wall; the receiving device is arranged in the first chamber, and the receiving device is used for receiving the medical waste and conveying the medical waste to the second chamber through the window; the output device is arranged in the second chamber, and the output device is used for receiving and conveying the medical waste; the conveyor belt is arranged in the second chamber, and the conveyor belt is used for driving the output device to move; a plurality of waste collection devices are arranged in the second chamber; the control device is used for distinguishing the types of the medical waste and controlling the output device to convey the medical waste to the corresponding waste collection device. By adopting the intelligent classified recovery system, a consulting room and a waste treatment room can be separated, the medical waste can be distributed to different waste collection devices, the environment of the consulting room is improved, and the working intensity is alleviated.