In this paper, we consider trajectory tracking control of a two-link flexible manipulator model in space. Two variables of joint angle and elastic deformation are partly decoupled by a nonlinear decoupling feedback control method. An extended state observer is introduced to estimate nonlinear terms of the two-link flexible manipulator system. Based on a back-stepping method, a nonlinear controller is designed for the flexible manipulator system. Finally, some simulation results are given to demonstrate the effectiveness of the developed techniques in this paper.