The invention discloses an error correction method of an autonomous navigation system. In the autonomous navigation system based on an ultraviolet earth sensor and a star sensor, the ultraviolet earth sensor is used for measuring a geocentric vector in a satellite local system, and the star sensor is used for measuring an attitude transformation matrix of the satellite local system. Since the sensors inevitably have relative installation error, and a filter cannot eliminate the system error, the navigation accuracy becomes poor. In the method provided by the invention, the relative installation error of the ultraviolet earth sensor and the star sensor is modeled, and the installation error is expanded into a state variable so as to perform navigation filtering. Assuming that the satellitecan obtain high-accuracy position measurement information by a GPS receiver or ground orbit determination within certain period of time, the system error can be estimated and corrected in time by filtering. The method provided by the invention has simple operation and can obviously improve the navigation accuracy.