The present invention discloses a system and method of unmanned aerial vehicle visual sense assistant position and flight control based on two-dimensional landmark identification. The system comprises an unmanned aerial vehicle body, a sensor module, a tracking locus generation module, a visual processing module, a sensor update module, a flight control module, a visual assist control switching module, an instruction output module and a camera. The two-dimensional marker arranged on the route specific position to perform visual extraction, an inertial navigation system is fused to perform calculation of accurate position and attitude information so as to assist and improve the precision of the GPS combination system, and diversification information guidance is provided for the unmanned aerial vehicle through two-dimensional encoding information to develop the diversity of a flight task. Besides, the present invention provides a cascade flight control system of adaptive compensation control based on deviation. The smooth transition of the marker identification state and the unidentification state is realized, the stability of the flight control is improved, and the accuracy of the identification is improved.