In this paper, modeling and controlling problem for a two-link rigid-flexible manipulator in three-dimensional (3D) space is studied under actuator faults. For modeling, the dynamics of the 3D mechanical system is represented by nonlinear partial differential equations, which is first derived in infinite dimension form. Based on the nonlinear model, the controller is proposed, which can achieve joint angle control and vibration suppression control in the presence of actuator faults. The stability analysis of the closed-loop system is given based on LaSalle invariance principle. Numerical simulations illustrate the effectiveness of the proposed controller. This study will promote the development of nonlinear flexible manipulator systems in 3D space. KEYWORDS actuator faults, nonlinear PDE model, two-link rigid-flexible manipulator, 3D space Int J Robust Nonlinear Control. 2019;29:3793-3807.wileyonlinelibrary.com/journal/rnc