Driven by the rise of intelligent manufacturing and Industry 4.0, the manufacturing industry faces significant challenges in adapting to flexible and efficient production methods. This study presents an innovative approach to solving the Flexible Job-Shop Scheduling Problem (FJSP) by integrating Heterogeneous Graph Neural Networks based on Relation (HGNNR) with Deep Reinforcement Learning (DRL). The proposed framework models the complex relationships in FJSP using heterogeneous graphs, where operations and machines are represented as nodes, with directed and undirected arcs indicating dependencies and compatibilities. The HGNNR framework comprises four key components: relation-specific subgraph decomposition, data preprocessing, feature extraction through graph convolution, and cross-relation feature fusion using a multi-head attention mechanism. For decision-making, we employ the Proximal Policy Optimization (PPO) algorithm, which iteratively updates policies to maximize cumulative rewards through continuous interaction with the environment. Experimental results on four public benchmark datasets demonstrate that our proposed method outperforms four state-of-the-art DRL-based techniques and three common rule-based heuristic algorithms, achieving superior scheduling efficiency and generalization capabilities. This framework offers a robust and scalable solution for complex industrial scheduling problems, enhancing production efficiency and adaptability.