The machining and assembly errors will result in misalignment between the real and nominal 3D models of aircraft panel. To solve the low position accuracy of holes caused by the misalignment, a positional error compensation method based on binocular vision measurement system is proposed. Firstly, the workflow of the robotic drilling system is introduced to choose a vision measurement system that can meet the drilling requirement. Then the component and the workflow of the vision measurement system are proposed. Finally, the coordinate extraction of datum holes, the error compensation of holes and database operation in the vision measurement system are introduced in detail. The positional error compensation method based on binocular vision measurement system can obtain the coordinate of datum holes, compensate the positional errors of holes, and write the compensation information in the database to enhance the position accuracy of holes.