Hyper-heuristic algorithms are known for their flexibility and efficiency, making them suitable for solving engineering optimization problems with complex constraints. This paper introduces a self-learning hyper-heuristic algorithm based on a genetic algorithm (GA-SLHH) designed to tackle the logistics scheduling problem of prefabricated modular cabin units (PMCUs) in cruise ships. This problem can be regarded as a multi-objective fuzzy logistics collaborative scheduling problem. Hyper-heuristic algorithms effectively avoid the extensive evaluation and repair of infeasible solutions during the iterative process, which is a common issue in meta-heuristic algorithms. The GA-SLHH employs a genetic algorithm combined with a self-learning strategy as its high-level strategy (HLS), optimizing low-level heuristics (LLHs) while uncovering potential relationships between adjacent decision-making stages. LLHs utilize classic scheduling rules as solution support. Multiple sets of numerical experiments demonstrate that the GA-SLHH exhibits a stronger comprehensive optimization ability and stability when solving this problem. Finally, the validity of the GA-SLHH in addressing real-world decision-making issues in cruise ship manufacturing companies is validated through practical enterprise cases. The results of a practical enterprise case show that the scheme solved using the proposed GA-SLHH can reduce the transportation time by up to 37%.