In response to the challenges of dynamic adaptability, real-time interactivity, and dynamic optimization posed by the application of existing deep reinforcement learning algorithms in solving complex scheduling problems, this study proposes a novel approach using graph neural networks and deep reinforcement learning to complete the task of job shop scheduling. A distributed multi-agent scheduling architecture (DMASA) is constructed to maximize global rewards, modeling the intelligent manufacturing job shop scheduling problem as a sequential decision problem represented by graphs and using a Graph Embedding–Heterogeneous Graph Neural Network (GE-HetGNN) to encode state nodes and map them to the optimal scheduling strategy, including machine matching and process selection strategies. Finally, an actor–critic architecture-based multi-agent proximal policy optimization algorithm is employed to train the network and optimize the decision-making process. Experimental results demonstrate that the proposed framework exhibits generalizability, outperforms commonly used scheduling rules and RL-based scheduling methods on benchmarks, shows better stability than single-agent scheduling architectures, and breaks through the instance-size constraint, making it suitable for large-scale problems. We verified the feasibility of our proposed method in a specific experimental environment. The experimental results demonstrate that our research can achieve formal modeling and mapping with specific physical processing workshops, which aligns more closely with real-world green scheduling issues and makes it easier for subsequent researchers to integrate algorithms with actual environments.