The invention discloses a small rotor unmanned aerial vehicle autonomous obstacle avoidance flight control system and a control method. The system comprises an autonomous flight control system, a ground station control system and a manual emergency intervention system. The autonomous flight control system comprises a flight control computer module, an obstacle detection module, a navigation and positioning module, a driving control module, an execution mechanism, an attitude reference module and a wireless communication link module. The ground station control system comprises a wireless data transmission link module and a ground control console. The manual emergency intervention system comprises a remote control receiver and a Futaba remote controller. A corresponding small rotor unmanned aerial vehicle autonomous obstacle avoidance flight control method is also provided. The autonomous obstacle avoidance flight control system is divided into three parts, a complete small rotor helicopter autonomous obstacle avoidance flight control system which integrates the autonomous flight control system, a dynamic flight path planning system and an emergency treatment mechanism as a whole is provided, and flight environment adaptability and job task universality are strong.