The invention discloses a control system used for environment-friendly and sanitation treatment equipment. The system comprises a micro controlling unit, a pipe detection probe unit, a remote control receiving unit, a key-press unit, a switch unit, a variable pressure power supply unit and a commercial power input port; the commercial power input port is connected with the switch unit and the variable pressure power supply unit through commercial power cords; the switch unit is connected with the environment-friendly and sanitation treatment equipment through the commercial power cords; the variable pressure power supply unit is connected with the micro controlling unit, the pipe detection probe unit, the remote control receiving unit and the switch unit through low pressure power cords; and the micro controlling unit is connected with the pipe detection probe unit, the remote control receiving unit, the key-press unit and the switch unit through signal lines. The invention further discloses a control method for the control system of the environment-friendly and sanitation treatment equipment. The control system has the advantages of intellectualization, convenient use, safety and reliability, low cost and high comprehensive property, can prevent misoperation, and executive the safety function.