The scene matching aided inertial integrated navigation system needs to get both the aircraft position errors and the course deviation relative to the present flight path simultaneously.A realtime scene matching algorithm based on region covariance was proposed.The distance of region covariance matrixs as the similarity measuring for image matching was introduced.Firstly,the image was smoothed by a Gaussion filter,and features of the image were extracted.Global searching algorithm using multilevel pyramid matching was put forward.Then,multiple local regions in real image was selected,and local searching and matching was utilized.The local match set between real image and referance image was obtained.Finally,the least square algorithm ans RANSAC method were applied to get the distortion transformation parameters between real image and referance image.The results of simulation show that the proposed image matching algorithm can satisfy the accuracy demands of scene aided navigation system and provide the system location and course errorcorrecting information.