Graph-based Retrieval-Augmented Generation (GraphRAG) has become the important paradigm for enhancing Large Language Models (LLMs) with external knowledge. However, existing approaches are constrained by their reliance on high-quality knowledge graphs: manually built ones are not scalable, while automatically extracted ones are limited by the performance of LLM extractors, especially when using smaller, local-deployed models. To address this, we introduce Think-on-Graph 3.0 (ToG-3), a novel framework featuring a Multi-Agent Context Evolution and Retrieval (MACER) mechanism. Its core contribution is the dynamic construction and iterative refinement of a Chunk-Triplets-Community heterogeneous graph index, powered by a Dual-Evolution process that adaptively evolves both the query and the retrieved sub-graph during reasoning. ToG-3 dynamically builds a targeted graph index tailored to the query, enabling precise evidence retrieval and reasoning even with lightweight LLMs. Extensive experiments demonstrate that ToG-3 outperforms compared baselines on both deep and broad reasoning benchmarks, and ablation studies confirm the efficacy of the components of MACER framework. The source code are available in https://github.com/DataArcTech/ToG-3.