The growing need for customized and varied production has highlighted the significance of smart and automated factories in the manufacturing sector. In this particular context, the scheduling of multiple Automated Guided Vehicles (AGVs) plays a pivotal role in enhancing the efficiency of operations within an intelligent manufacturing shop. This study centers on the material handling process within a matrix manufacturing shop with the objective of identifying the most cost-effective transportation routes for materials. To accomplish the specified objective, this research aims to identify an optimal solution for reducing transportation costs. In particular, this study formulates a mixed-integer linear programming model and introduces a novel discrete variant of the moth-flame optimization (MFO) algorithm, named DMFO, to address the scheduling problem. The DMFO algorithm incorporates several significant enhancements. Firstly, a population initialization method is proposed, which combines a nearest-neighbor-based adaptive heuristic and a random sorting technique to ensure the formation of a well-structured population. Secondly, the flame generation mechanism and spiral flight search processes within the MFO have been redefined to achieve a more optimal balance between exploration and exploitation. A neighborhood search mechanism is subsequently devised, employing the concept of neighborhood relevance to accelerate the convergence process. Additionally, a heuristic approach is introduced to reduce the computational cost. Moreover, a population regeneration mechanism is proposed to avoid the algorithm falling into a local optimum. To validate the effectiveness of the DMFO, a comparative analysis is conducted using a dataset of 110 real-world factory instances. In this analysis, eight well-established optimization algorithms are employed. The simulation results consistently demonstrate that the relative percentage deviation (RPD) value of the DMFO tends to approach 0% more closely compared to other algorithms, thereby substantiating the effectiveness of the proposed algorithm.