Retrieval-Augmented Generation (RAG) has emerged as a powerful framework for enhancing the capabilities of Large Language Models (LLMs) by integrating retrieval-based methods with generative models. As external knowledge repositories continue to expand and the parametric knowledge within models becomes outdated, a critical challenge for RAG systems is resolving conflicts between retrieved external information and LLMs' internal knowledge, which can significantly compromise the accuracy and reliability of generated content. However, existing approaches to conflict resolution typically operate at the token or semantic level, often leading to fragmented and partial understanding of factual discrepancies between LLMs' knowledge and context, particularly in knowledge-intensive tasks. To address this limitation, we propose TruthfulRAG, the first framework that leverages Knowledge Graphs (KGs) to resolve factual-level knowledge conflicts in RAG systems. Specifically, TruthfulRAG constructs KGs by systematically extracting triples from retrieved content, utilizes query-based graph retrieval to identify relevant knowledge, and employs entropy-based filtering mechanisms to precisely locate conflicting elements and mitigate factual inconsistencies, thereby enabling LLMs to generate faithful and accurate responses. Extensive experiments reveal that TruthfulRAG outperforms existing methods, effectively alleviating knowledge conflicts and improving the robustness and trustworthiness of RAG systems.