The flexible robotic drilling system has been widely used in the aircraft industry in recent years. There are three ways to attach an end-effector to a robot, which are the pointing configuration, the hanging configuration, and the side configuration. The simulation model of robot and workpiece is constructed by using MATLAB software. According to the three configurations, reachability, manipulability, joint useability, and joint passive torque of a robot are calculated by means of the MATLAB language. Based on the calculation results and various measures, the performance, including reachability, manipulability, joint useability, and deformation, of a robot are analyzed. The analysis results show that the pointing configuration has the best reachability, a long service life, and small energy consumption, and it substantially reduces the fifth axis joint passive torque produced by the clamp force, which will improve positional accuracy of holes; the hanging configuration and the side configuration improve robot's manipulability and are suitable for drilling in the curved surface.