A carbon/glass hybrid fiber continuous sucker rod (CR) with lower specific gravity, better corrosion resistance and higher strength was developed to replace the steel rod in oil production. This paper proposes a multi-objective holistic optimization method of sucker rod pumping system (SRPS) using CR for improving oil recovery benefits. Firstly, based on the cross-scale failure criterion and finite element simulation, a judgment index for fatigue damage of CR and their joints under multiple loads, namely fatigue strength margin (FSM), is constructed, and used as a life characterization parameter of SRPS. After it is verified with liner correlation between the production cycle and FSM of realistic SRPS, FSM in addition to energy consumption and the production rate are included in the optimization objectives. Then, a multi-objective optimization model with the holistic parameters of CR SRPS as the decision variables is established. To improve the efficiency of solving the model, a hierarchical enumeration algorithm with the strategy of reducing the optimization space repeatedly by weakened constraints is presented. Finally, the proposed method was applied to the design of CR SRPS for realistic oil wells, its effectiveness and superiority are verified by the application effect and comparison results with current methods.