This paper proposed a multi-objective, multi-disciplinary design optimization and multi-attribute evaluation method for the manned lunar lander descent stage. A system design model is established considering multiple disciplines such as propulsion, structure, trajectory and cost. With the goal of minimizing mass, minimizing cost and maximizing velocity increment, the overall scheme for hybrid rocket motors was optimized by altering various grain shapes and feed systems, acting as an alternative propulsion scheme for the manned lunar lander. Under the same design conditions, the optimal scheme of hybrid rocket motors considering continuous and discrete attributes was studied and compared with that of liquid rocket engines to elucidate the characteristics of the hybrid rocket motors for deep space exploration. The results showed that the evaluation results obtained by considering only continuous attributes were different from those by considering both continuous and discrete attributes. The liquid propulsion scheme with liquid oxygen/kerosene is superior to the hybrid propulsion schemes due to its excellent cost and specific impulse performance when only continuous attributes are considered. However, hybrid rocket motors have shown good performance in terms of operability, manufacturability, safety and environmental protection. So, after introducing discrete attributes, the hybrid propulsion schemes show greater potential. In brief, based on the multi-attribute evaluation method considering comprehensive attributes, the hybrid rocket motor provided with tube grain and gas pressure feed system was considered as the optimal propulsion system for the lunar lander. Furthermore, the parametric analysis showed that the fuel grain outside diameter, the initial design thrust and the initial oxygen-to-fuel ratio had a significant influence on the performance of the hybrid rocket motor for the lunar lander, and in particular, the effect of the fuel grain outside diameter was more than 50%.