Collaborative robots are becoming more and more widely used, with a common feature–lightweight. In order to achieve this objective, the modular joints become the core part of the collaborative robots. However, the modular joints integrate various components, such as torque sensors and harmonic drives, which not only inevitably introduce joint flexibility but induce mechanical vibration easily. Therefore, with the purpose of suppressing vibration of the modular joint, a robust method based on the equivalent rigid body state observer is proposed, in which the equivalent rigid body velocity as a state variable is indirectly obtained. This method improves robustness to the load inertia changes in a limit range compared to the traditional equivalent rigid body velocity method. The effective of this method is confirmed by simulation in this paper.