This paper presents a two-step approach for optimizing the configuration of a mobile photovoltaic-diesel-storage microgrid system. Initially, we developed a planning configuration model to ensure a balance between the mobility of components and a sustainable power supply. Then, we introduced a method that merges optimization and decision-making. The first phase identifies Pareto optimal solutions (POSs) with a favorable distribution by using a multi-objective evolutionary algorithm with classification-based preselection (CPS-MOEA). In the second phase, we utilize the fuzzy C-means algorithm (FCM) and the grey relational projection (GRP) method for comprehensive decision-making. This aims to select the most suitable and compromise solution from the POSs, closely aligning with the decision-maker’s preferences. Beyond addressing the optimal planning and configuration issue, the experimental results show that the method surpasses other widely used multi-objective optimization algorithms, including the Preference Inspired Co-evolution Algorithm (PICEA-g), the Multi-Objective Particle Swarm Optimization Algorithm (MOPSO), and the third stage of Generalized Differential Evolution (GDE3).