Graph-based Retrieval-Augmented Generation (GraphRAG) enhances the reasoning capabilities of Large Language Models (LLMs) by grounding their responses in structured knowledge graphs. Leveraging community detection and relation filtering techniques, GraphRAG systems demonstrate inherent resistance to traditional RAG attacks, such as text poisoning and prompt injection. However, in this paper, we find that the security of GraphRAG systems fundamentally relies on the topological integrity of the underlying graph, which can be undermined by implicitly corrupting the logical connections, without altering surface-level text semantics. To exploit this vulnerability, we propose LogicPoison, a novel attack framework that targets logical reasoning rather than injecting false contents. Specifically, LogicPoison employs a type-preserving entity swapping mechanism to perturb both global logic hubs for disrupting overall graph connectivity and query-specific reasoning bridges for severing essential multi-hop inference paths. This approach effectively reroutes valid reasoning into dead ends while maintaining surface-level textual plausibility. Comprehensive experiments across multiple benchmarks demonstrate that LogicPoison successfully bypasses GraphRAG’s defenses, significantly degrading performance and outperforming state-of-the-art baselines in both effectiveness and stealth. Our code is available at <https://github.com/Jord8061/logicPoison>.

Graph-based Retrieval-Augmented Generation (GraphRAG) advances flat document retrieval by structuring knowledge as relational graphs, enabling more coherent and effective reasoning. However, applying it to specific domains like legal reasoning faces critical challenges. (i) Legal corpora are heterogeneous, containing multi-granular knowledge from cases, articles and interpretations. A flat knowledge graph cannot adequately differentiate between factual details, applied rules, and abstract principles, limiting accurate retrieval. (ii) Reliable legal judgment demands transparent, evidence-based reasoning. Traditional RAG passes retrieved context directly to an LLM without verification, resulting in opaque, error-prone reasoning. To this end, we propose LegalGraphRAG, a framework designed for reliable legal reasoning. Our approach introduces two core components: a hierarchical legal graph that hierarchically organizes legal sources to enable retrieval at appropriate abstraction levels, and a multi-agent system for reliable legal reasoning, where a Researcher retrieves candidate evidence, an Auditor rigorously verifies its validity against source documents, and an Adjudicator synthesizes the set of verified evidence to render a final judgment. Extensive experiments show that LegalGraphRAG achieves the state-of-the-art performance, outperforming existing GraphRAG baselines in accurate and trustworthy legal analysis. Our code, datasets and implementation details are available at https://github.com/XMUDeepLIT/LegalGraphRAG.