In this paper, a novel distributed hierarchical control method for small satellites with multiple disturbances and input constraints is investigated by combining formation flying and satellite cluster. First, a finite-time convergent extended state observer (FTCESO) is developed to estimate the external disturbance with high precision, and a non-singular fast terminal sliding mode controller (NFTSMC) is proposed to maintain the specific configuration of leader-satellites and the finite time convergence is theoretically proved. Then, an improved artificial potential field method with collision avoidance and damping characteristics is proposed for the follower-satellite, so that the follower-satellite can keep a collision-avoidance relative distance from corresponding leader-satellite with the desired communication range. Finally, numerical simulations are performed to demonstrate the effectiveness of the proposed method.