The robust control scheme based on velocity filter of free-floating dual-arm space robot system with uncertain payload parameters was studied. Through the Lagrangian approach, the dynamic equation of the free-floating space robot was modeled as under-actuated system. With the augmentation approach, it was demonstrated that the dynamic equations and the augmented generalized Jacobi matrix of the system can be linearly dependent on a group of inertial parameters, respectively. Based on the results, a robust controller based on velocity filter was developed for dual-arm space robot system with uncertain payload parameters to track the desired trajectories in inertial space. Ascribe to the pseudo-velocity signal acquired through the velocity filter, the proposed control scheme with only accurate positions of the joints and the end-effectors feedback avoid measuring the velocity and acceleration of the end-effectors. And it can avoid the control chatter effectively at the same time. The effect of the controller is testified by computer simulation.