In recent years, mixed-model assembly lines (MMALs) have been widely adopted by the automotive enterprises to face the requirements of mass customization. Meanwhile, the diversified components of various end products are placing the material feeding processes at great challenges. Under this circumstance, to raise the material feeding efficiency, this paper proposes an automatic monorail shuttle system (AMSS) based on line-integrated supermarkets applied to the MMALs by introducing the load-exchangeable shuttles and crossovers. Considering the importance of cost-control in manufacturing enterprises, we establish a mathematical model with the objective to minimize the total costs of the material feeding system, which includes the installation costs of crossovers and the input and operation costs of load-exchangeable shuttles. Then, due to the NP-hard nature of the proposed problem, a shuffled frog leaping-based hyper heuristic (SBHH) algorithm is developed to determine the allocation and scheduling of the shuttles and crossovers, which adopts the shuffled frog leaping algorithm (SFLA) as the high-level heuristic to select the low-level heuristics. To improve the performance of the algorithm, the concept of ‘dynamic decision unit’ is presented to raise the solution accuracy and the convergence speed. Finally, the simulation results verified the superiority of the proposed SBHH algorithm both in solution quality and convergence speed by comparing with other optimization algorithm in the existing literature.