Large language models (LLMs) excel in question-answering (QA) tasks, and retrieval-augmented generation (RAG) enhances their precision by incorporating external evidence from diverse sources like web pages, databases, and knowledge graphs. However, current RAG methods rely on agent-specific strategies for individual data sources, posing challenges low-resource or black-box environments and complicates operations when evidence is fragmented across sources. To address these limitations, we propose ER-RAG, a framework that unifies evidence integration across heterogeneous data sources using the Entity-Relationship (ER) model. ER-RAG standardizes entity retrieval and relationship querying through ER-based APIs with GET and JOIN operations. It employs a two-stage generation process: first, a preference optimization module selects optimal sources; second, another module constructs API chains based on source schemas. This unified approach allows efficient fine-tuning and seamless integration across diverse data sources. ER-RAG demonstrated its effectiveness by winning all three tracks of the 2024 KDDCup CRAG Challenge, achieving performance on par with commercial RAG pipelines using an 8B LLM backbone. It outperformed hybrid competitors by 3.1% in LLM score and accelerated retrieval by 5.5X.