Aiming at the problem of complex structure and high fault occurrence in the attitude control system of launch vehicle, a multiple model fault detection and isolation algorithm was proposed. The small deviation attitude dynamics model of the launch vehicle was established, and the Kalman filter of the system was designed. Combined with the idea of special observer, multiple Kalman filter banks with different structures were used to generate corresponding residuals, so that a single residual was only sensitive to a fault of the sensor or actuator. The fault isolation strategy was deduced theoretically to achieve the detection and isolation of different fault types of the launch vehicle. Simulation analysis shows that when no fault occurs, the residual results do not exceed the set threshold, and the algorithm does not alarm; when the sensor or actuator fails, the proposed isolation strategy can accurately locate the fault, which verifies the effectiveness of the algorithm.