The invention discloses a water quality monitoring system based on an unmanned ship. The water quality monitoring system comprises an unmanned ship, wherein at least one group of detection unit is arranged on the unmanned ship; the detection unit comprises a water collection pipe, a water collection pump, a flow divider valve connected with the water collection pipe, and four detection cavities connected with the flow divider valve; a sensor is arranged in each detection cavity; the flow divider valve comprises a valve body with a cavity inside; a cylindrical valve core is arranged in the cavity; a rotary shaft is mounted on the axis of the valve core; the rotary shaft is mounted at a power output end of a motor; the valve core can rotate under the drive of the motor. According to the water quality monitoring system based on the unmanned ship disclosed by the invention, unnecessary loss of the sensor can be avoided, the monitoring cost is reduced, and the sensor changing frequency is reduced.