Urban commuting flow prediction is crucial for urban planning, transportation optimization, and supply chain management. Traditional models and machine learning solutions often fall short in capturing the complex dynamics of urban mobility, overlooking factors like spatial correlation and human mobility patterns. Recent deep learning advancements have shown promise by integrating spatial correlation through incorporating geographical adjacency. However, this approach may not fully capture spatial correlation, particularly the semantic adjacency effect of zones connected via public transportation lines, such as metro networks—a novel dimension overlooked in prior research. The metro station serves as a major transit hub, attracting passengers from various origins and destinations and correlating the flow between the connected zones and other zones within the metro network. Devising an optimized model to encapsulate these spatial correlations is another crucial area of research where scientists are actively seeking the most effective solutions. We propose a novel sequential hybrid approach leveraging graph-based learning, focusing on the underexplored impact of metro networks on commuting flow prediction. Our model integrates two types of adjacency—geographic and semantic—using Graph Convolutional Networks (GCNs) to embed geographic correlations among proximate zones and Graph Attention Networks (GATs) to incorporate semantic adjacency defined by metro line connectivity. Furthermore, our approach innovatively incorporates features directly from online maps, eliminating reliance on third-party resources and enhancing scalability and efficiency. We validate our model using real-world datasets from Montreal, Canada, comprising travel surveys and GPS trajectory types, totaling nearly 900,000 trip records. Through evaluation using established performance metrics such as MAE, RMSE, MAPE, and CPC, we demonstrate significant improvement in predictive accuracy compared to existing state-of-the-art models. Our research has practical implications for urban planning and infrastructure development, aiding policymakers and urban planners in analyzing the impact of new urban infrastructure on commuting flow dynamics and facilitating informed decisions regarding transportation and infrastructure planning.