To the navigation of Unmanned Aerial Vehicle(UAV) in the complex unknown environment, an algorithm of position and attitude estimation based on the binocular stereo vision is described in this paper. Stereo vision pairs are taken by the binocular camera. The feature points are detected with the Harris algorism after the stereo vision pairs are rectified and the feature points are matched with NCC algorithm. Then the 3D stereo information of the feature points can be calculated in the camera coordinate system and the position and attitude of UAV are estimated with RANSAC algorithm and L-M iteration algorithm. The result of the experiment shows that the position and attitude estimation algorithm based on binocular stereo vision has strong adaptability of the unknown environment. Compared to the real position and attitude, there is a small error. The algorithm can meet the requirements of UAV navigation. A new way can be provided for the UAV navigation.