Abstract: China’s deep space exploration program is a complex and systematic project involving many fields and having great technical difficulties and funding requirements. The current program optimization method was developed in response to the demonstration group’s demonstration and the expert evaluation of the intermediary agency. This method requires a long demonstration period and makes rapid scientific decisions difficult. The Analytic Hierarchy Process (AHP) and the Fuzzy Analytic Hierarchy Process (FAHP) are both practical multi-factor and multi-objective decision-making methods that are widely used in many fields. To solve the problem of AHP being difficult to verify and judge for consistency, the concept of a fuzzy, consistent matrix was introduced, followed by the establishment of the FAHP. The introduction of the FAHP into the optimization of the overall scheme for deep space exploration benefits both the selection of the optimal overall scheme at the national level, which enables all relevant parties to reach consensus as soon as possible, and the national scientific decision-making process. This study established a systematic index evaluation model based on the FAHP model, considering the multi-index and multi-level structure of technology, science, and funding, among other things. By combining expert judgment and theoretical analysis, a judgment matrix of indicators at various levels was established and weight coefficients were derived for the Chang’e-4 mission plan in China’s lunar exploration project. Then, the overall plan was evaluated for optimal applicability. The results show that the three factors of technology, science, and funding are more important than time and benefit. Advancement and reliability are the primary control factors under the technical criteria. Scientific value is the major controlling factor when it comes to scientific criteria. The development cost is the primary constraint on the funding criterion. Planning compliance and planning feasibility are the primary controlling factors under the cycle criterion. Scientific output and technological promotion are the major controlling factors under the criterion of benefit. Among the four alternatives, the one in which the relay satellite is launched by the Long March 4C and the lander and rover are launched by the Long March 3B has the largest sorting weight. As a result, this solution is the optimal solution that is also consistent with the current situation. This research can help China provide rapid and scientifically sound support for various deep space exploration programs.