The paper presents an angular acceleration planning method for joint space of manipulator to achieve real-time tracking tasks under joint constraint. To improve the performance of the algorithm and ensure the joint limit, the proposed method establishes a Second-order System with Variable Impedance (SSVI). The Second-order System is introduced in the joint space through the joint angular acceleration in second derivative of kinematics. The impedance parameters vary with different states of joint and the variable impedance produced virtual repulsive force to ensure that the joint motions are within the specified ranges when they are close to limits. The damping impedance contained in the system can improve convergence speed and suppress system oscillation and vibration caused by factors such as the visual noise. Simulation and experiment results verify that the method is effective and has faster convergence speed and more smooth motion compared with other methods.