In this paper, we propose a systematic framework for the autonomous navigation system based on distributed filtering for an Unmanned Aerial Vehicle (UAV). The proposed framework consists of the design and algorithm of the autonomous navigation. Therein, the camera mounted on the UAV functions as a navigation sensor targeted for navigation and positioning. In order to reduce the computational complexity and exclude the risk caused by Global Positioning System (GPS) outage, an autonomous navigation system based on distributed filtering is designed and realized. When GPS is available by monitoring the GPS integrity, sensor information from Strapdown Inertial Navigation System (SINS) and GPS is fused using a 7-state Conventional Kalman Filter (CKF) to estimate the full UAV state (position, velocity and attitude); when GPS is unavailable, sensor information from gyroscopes, accelerometers and magnetometer is fused using a 4-state Extended Kalman Filter (EKF) to estimate the attitude and heading of the UAV, and sensor information from SINS and vision positioning system is fused using a 7-state Incoordinate Interval Kalman Filter (IIKF) to estimate the position and velocity of the UAV. In addition, the second-order vertical channel damping loop is adopted to fuse measurements from a barometer with those of SINS, which suppresses the divergence of the vertical channel error and makes the altitude information calculated by SINS trustable. Both ground and flight experiments of the autonomous navigation system have been carried out. The test results show that the system can provide stabilized attitude information in long durations, and can realize the automatic flight control of UAV.