Retrieval Augmented Generation enhances the response accuracy of Large Language Models (LLMs) by integrating retrieval and generation modules with external knowledge, demonstrating particular strength in real-time queries and Visual Question Answering tasks. However, the effectiveness of RAG is frequently hindered by the precision of the retriever: many retrieved samples fed into the generation phase are irrelevant or misleading, posing a critical bottleneck to LLMs’ performance. To address this challenge, we introduce \textbf{VaccineRAG}, a novel Chain-of-Thought-based retrieval-augmented generation dataset. On one hand, VaccineRAG employs a benchmark to evaluate models using data with varying positive/negative sample ratios, systematically exposing inherent weaknesses in current LLMs. On the other hand, it enhances models’ sample-discrimination capabilities by prompting LLMs to generate explicit Chain-of-Thought (CoT) analysis for each sample before producing final answers. Furthermore, to enhance the model’s ability to learn long-sequence complex CoT content, we propose \textbf{Partial-GRPO}. By modeling the outputs of LLMs as multiple components rather than a single whole, our model can make more informed preference selections for complex sequences, thereby enhancing its capacity to learn complex CoT. Comprehensive evaluations and ablation studies on VaccineRAG validate the effectiveness of the proposed scheme. The code and dataset will be publicly released soon.