Three-dimensional (3D) printing, also known as additive manufacturing, has unique advantages over traditional manufacturing technologies; thus, it has attracted widespread attention in the medical field. Especially in the context of the frequent occurrence of major public health events, where the medical industry's demand for large-scale and customized production is increasing, traditional 3D printing production scheduling methods take a long time to handle large-scale customized medical 3D printing (M-3DP) production and have weak intelligent collaboration ability in the face of job-to-device matching under multimaterial printing. Given the problem caused by M-3DP large-scale customized production scheduling, an intelligent collaborative scheduling multiagent-based method is proposed in this study. First, a multiagent-based optimization model is established. On this basis, an improved genetic algorithm embedded with the product mix strategy and the intelligent matching mechanism is designed to optimize the completion time and load balance between devices. Finally, the effectiveness of the proposed method is evaluated using numerical simulation. The simulation results indicated that compared with the simple genetic algorithm, particle swarm optimization, and snake optimizer, the improved genetic algorithm could better reduce the M-3DP mass customization production scheduling time, optimize the load balance between devices, and promote the “intelligent manufacturing” process of M-3DP mass customization.