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In this study, we propose a new design method of motion and external force trajectories for the rehabilitation of inner shoulder muscles based on the biomechanical analysis of the upper limbs. The method is assumed to use a robot manipulator; therefore, it enjoys the advantage of providing 3-dimensional trajectories and applied forces to the patient. Both the trajectories of rehabilitation motion and the applied force by the robot are designed in the same planning stage, in order to maximize the rehabilitation efficiency evaluation function based on the biomechanical analysis of the patient for each joint's torque, each muscle's force, and each joint's reaction force. In order to focus the spotlight on the advantages of the proposed robot-aided method, an example is given for comparison with a weight-based method which is supposed to use a weight for providing force to the patient. The comparison demonstrates the advantage of the proposed method in a quantitative manner from several rehabilitation points of view.