The invention provides an autonomous precision landing system of an unmanned aerial vehicle on a motion platform and a landing method. The autonomous precision landing system comprises a rotor unmanned aerial vehicle 1, an airborne platform camera 2, an airborne computer 3, airborne undercarriage magnetic devices 4, a vehicle-mounted iron ground 6 and a multi-layer nested identifier 7, wherein the multi-layer nested identifier 7 is composed of two-dimensional codes which are mutually overlapped, different in size, different in pattern and asymmetric in distribution; the two-dimensional codes with a small size cover the two-dimensional code with a large size; the two-dimensional code with a large size is covered with a plurality of two-dimensional codes with a small size along the advancing direction of a motor vehicle 5, and the number of the two-dimensional code with the maximum size is only one. According to the invention, the platform camera carried by the rotor unmanned aerial vehicle is utilized, the multi-layer nested identifier 7 is recognized by adopting the airborne platform camera 2, a vision-assisted rotor unmanned aerial vehicle autonomous landing system which is high in precision, good in reliability and low in cost is provided, and the system is particularly applicable to landing at the top end of a moving motor vehicle.