This paper addresses the problems of trajectory tracking control of a reconfigurable manipulator with harmonic drive transmission under a decentralized integral sliding mode control method, and a high-performance control is achieved based on adaptive super-twisting algorithm. First, the dynamic model of the reconfigurable manipulator is formulated with a nonlinear harmonic drive model. Second, based on only local dynamic information of each module, a decentralized controller is designed to reduce the chattering effect of the joint module and compensating the model uncertainty. The stability of the close-loop system is proved by using the Lyapunov theory. Finally, simulations are performed for a 3-DOF reconfigurable manipulator to study the advantage of the proposed method.