The increasing complexity, adaptability, and interconnections inherent in modern manufacturing systems have spurred a demand for integrated methodologies to boost productivity, improve quality, and streamline operations across the entire system. This paper introduces a holistic system-process modeling and control approach, utilizing a Multi-Agent Reinforcement Learning (MARL) based integrated control scheme to optimize system yields. The key innovation of this work lies in integrating the theoretical development of manufacturing system-process property understanding with enhanced MARL-based control strategies, thereby improving system dynamics comprehension. This, in turn, enhances informed decision-making and contributes to overall efficiency improvements. In addition, we present two innovative MARL algorithms: the credit-assigned multi-agent actor-attention-critic (C-MAAC) and the physics-guided multi-agent actor-attention-critic (P-MAAC), each designed to capture the individual contributions of agents within the system. C-MAAC extracts global information via parallel-trained attention blocks, whereas P-MAAC embeds system dynamics through permanent production loss (PPL) attribution. Numerical experiments underscore the efficacy of our MARL-based control scheme, particularly highlighting the superior training and execution performance of C-MAAC and P-MAAC. Notably, P-MAAC achieves rapid convergence and exhibits remarkable robustness against environmental variations, validating the proposed approach’s practical relevance and effectiveness.