The invention discloses a water quality automatic sampling system based on a rotor unmanned plane and a method thereof, and applicable to the technical field of water quality sampling and detection. The water quality automatic sampling system mainly comprises a turntable motor (1), a depth detecting sensor (9), a sampling pump (12), a sampling bottle (16), a solenoid valve (17), an unmanned plane (19), a rocker arm (20), and a controller (21); the turntable motor drives the sampling pipe and adjusts the sampling depth; the sampling pipe is connected with a plurality of sampling bottles through a branch, and the sampling bottles are arranged in the middle of the sampling platform base; the platform base is connected with the unmanned plane through the rocker arm; through bending the rocker arm, the flying model and the traction model of the unmanned vehicle can be switched; compensation bending is performed on the rocker arm monitored and controlled on the basis of a gradiograph. The system and the method can realize the organic combination of water quality sampling and the unmanned vehicle, fully use the loading and cruising ability of the unmanned vehicle, effectively keep the balance property of the sampling system, and are featured by fast sampling, convenience, and high efficiency.