Disturbance is a critical influence to the low earth orbit satellites formation. Cooperative control for the configuration and attitude of formation is also troubled with the disturbances in the model, which mainly contain space environment perturbations, flexible appendages and disturbance from various styles actuators of the satellite. In this paper, hybrid dynamics model of relative position and attitude is built and different disturbances are analyzed, which include the J2 and atmospheric drag perturbations, flexible appendages vibration and cross-coupled disturbance caused by thrusters. Then an effective anti-disturbance cooperative controller is proposed to achieve relative position keeping and small attitude angle tracking simultaneously. The controller consists of disturbance observer combined with H∞ state feedback. Based on Lyapunov theorem, the stabilization of the system is proved. Finally, numerical simulations and semi-physical tests are conducted with supports of the engineering simulators and air hovered turntable. The results show that the control method presented is effective for the satellites formation position/attitude co-operation, and the accuracy and stabilization can be also satisfied.