This Special Issue reprint presents recent advances in the design, modeling, optimization, and control of manufacturing systems, with a focus on innovative and practical approaches relevant to both academia and industry. Contributions cover a wide range of topics including intelligent scheduling, simulation-based optimization, human-centered production, collaborative robotics, and sustainable system design. The selected papers reflect the increasing complexity of modern production environments and the growing importance of integrating artificial intelligence, cyber-physical systems, and data-driven decision-making. An emphasis is placed on methodological rigor as well as real-world applicability, making this reprint a valuable reference for researchers, engineers, and practitioners engaged in manufacturing system improvement and transformation. By showcasing both theoretical insights and applied case studies, this collection offers a comprehensive overview of current trends and challenges in the field.