Intelligent Transportation Systems (ITSs) have emerged as a promising solution towards ameliorating urban traffic congestion, with Traffic Signal Control (TSC) identified as a critical component. Although Multi-Agent Reinforcement Learning (MARL) algorithms have shown potential in optimizing TSC through real-time decision-making, their scalability and effectiveness often suffer from large-scale and complex environments. Typically, these limitations primarily stem from a fundamental mismatch between the exponential growth of the state space driven by the environmental heterogeneities and the limited modeling capacity of current solutions. To address these issues, this paper introduces a novel MARL framework that integrates Dynamic Graph Neural Networks (DGNNs) and Topological Data Analysis (TDA), aiming to enhance the expressiveness of environmental representations and improve agent coordination. Furthermore, inspired by the Mixture of Experts (MoE) architecture in Large Language Models (LLMs), a topology-assisted spatial pattern disentangling (TSD)-enhanced MoE is proposed, which leverages topological signatures to decouple graph features for specialized processing, thus improving the model's ability to characterize dynamic and heterogeneous local observations. The TSD module is also integrated into the policy and value networks of the Multi-agent Proximal Policy Optimization (MAPPO) algorithm, further improving decision-making efficiency and robustness. Extensive experiments conducted on real-world traffic scenarios, together with comprehensive theoretical analysis, validate the superior performance of the proposed framework, highlighting the model's scalability and effectiveness in addressing the complexities of large-scale TSC tasks.