In order to maintain and enhance the operational reliability of a robotic manipulator deployed in space, an operational reliability system control method is presented in this paper. First, a method to divide factors affecting the operational reliability is proposed, which divides the operational reliability factors into task-related factors and cost-related factors. Then the models describing the relationships between the two kinds of factors and control variables are established. Based on this, a multivariable and multiconstraint optimization model is constructed. Second, a hierarchical system control model which incorporates the operational reliability factors is constructed. The control process of the space manipulator is divided into three layers: task planning, path planning, and motion control. Operational reliability related performance parameters are measured and used as the system’s feedback. Taking the factors affecting the operational reliability into consideration, the system can autonomously decide which control layer of the system should be optimized and how to optimize it using a control level adjustment decision module. The operational reliability factors affect these three control levels in the form of control variable constraints. Simulation results demonstrate that the proposed method can achieve a greater probability of meeting the task accuracy requirements, while extending the expected lifetime of the space manipulator.