The invention provides a fault tolerance flight control system based on control surface faults. The fault tolerance flight control system based on control surface faults comprises a sensor, a fault detection and insulation module, a monitor module, a controller module and a control distribution module, wherein the sensor is arranged at the corresponding part of an airplane body; the fault detection and insulation module transmits an airplane state parameter estimation value to the controller module, judges the health situation of control surfaces and the types of the generated faults, calculates the probability of the type of faults on each control surface, transmits the probability to the monitor module, detects the deviation angle of each control surface to obtain a deviation angle estimation value of each control surface, and transmits the deviation angle estimation value of each control surface to the monitor module; the monitor module determines the faults positions of the control surfaces, and provides a control distribution basis for the control distribution module; the controller module generates a virtual control command vector, and transmits the vector to the control distribution module as virtual control input; the control distribution module calculates the control surface deviation angle vector of each control surface deviation angle given value. When the control surface faults occur, based on fault detection and diagnosis results, the fault tolerance flight control system based on control surface faults provided by the invention compensates faults, thereby guaranteeing the continuous and safe flight of an airplane.