Nuclear-powered turbojet engine has excellent application prospects in the field of aviation propulsion power system due to its advantages of ultra long endurance, huge driving force, high energy density, no carbon emissions and small fuel weight. The selection of cycle mode and cycle working medium has a strong impact on its operation and safety performance, size, weight and economy, and relevant evaluation research is important. In this paper, the self-developed thermal hydraulic analysis program, size model, weight model and economic model are used to carry out the comparative analysis of the key operating parameter, size, weight and cost for the indirect cycle with different cycle working mediums and the direct cycle. Finally, the best scheme of nuclear-powered turbojet engine is obtained through comprehensive comparative analysis. The results show that the indirect cycle of the specific working medium is superior to the direct cycle. According to the constraints between the key operating parameters of the indirect cycle, the optimal operating parameters of the indirect cycle can be obtained. Through comprehensive evaluation in various aspects, indirect cycle (He) is evaluated as the optimal scheme of nuclear-powered turbojet engine. The relevant research results provide theoretical reference and support for the scheme design of nuclear-powered turbojet engine.