Graph-RAG constructs a knowledge graph from text chunks to improve retrieval in Large Language Model (LLM)-based question answering. It is particularly useful in domains such as biomedicine, law, and political science, where retrieval often requires multi-hop reasoning over proprietary documents. Some existing Graph-RAG systems construct KNN graphs based on text chunk relevance, but this coarse-grained approach fails to capture entity relationships within texts, leading to sub-par retrieval and generation quality. To address this, recent solutions leverage LLMs to extract entities and relationships from text chunks, constructing triplet-based knowledge graphs. However, this approach incurs significant indexing costs, especially for large document collections. To ensure a good result accuracy while reducing the indexing cost, we propose KET-RAG, a multi-granular indexing framework. KET-RAG first identifies a small set of key text chunks and leverages an LLM to construct a knowledge graph skeleton. It then builds a text-keyword bipartite graph from all text chunks, serving as a lightweight alternative to a full knowledge graph. During retrieval, KET-RAG searches both structures: it follows the local search strategy of existing Graph-RAG systems on the skeleton while mimicking this search on the bipartite graph to improve retrieval quality. We evaluate 13 solutions on three real-world datasets, demonstrating that KET-RAG outperforms all competitors in indexing cost, retrieval effectiveness, and generation quality. Notably, it achieves comparable or superior retrieval quality to Microsoft's Graph-RAG while reducing indexing costs by over an order of magnitude. Additionally, it improves the generation quality by up to 32.4% while lowering indexing costs by around 20%.