In this paper, the distributed attitude synchronization control problem is addressed for satellite formation flying system (SFFS) with external disturbance and actuator misalignment by using adaptive terminal sliding mode control (ATSMC) technique. The satellite attitude system model considered in this paper is transformed into a lagrange nonlinear system. On this basis, a terminal sliding mode surface is designed for the attitude tracking error of SFFS, then a novel adaptive terminal sliding mode control scheme base on neural networks is developed, such that the satisfactory formation flying performance could be achieved in existence of external disturbance. Meanwhile, the obtained ATSMC scheme are extended to the actuator misalignment case, and Lyapunov stability theory is used to prove the stability and synchronization of the whole closed loop SFFS. The simulation results are given to demonstrate the effectiveness and superiority of the proposed control strategy.