Long-document question answering is challenging because relevant evidence is often scattered across distant sections. Traditional long-document QA/RAG pipelines often suffer from context fragmentation, retrieving locally plausible but structurally misaligned passages. We present the Hierarchical Quantized Document Retriever (HQDR), a framework that aligns hierarchical graph representations with a universal token vocabulary and integrates explicit structure into retrieval. By grounding continuous structural features in a fixed, discrete semantic space, HQDR captures universal hierarchical patterns rather than overfitting to specific layouts. We further propose a hybrid scoring mechanism that decouples semantic matching from structural alignment. Extensive experiments on QASPER and Natural Questions demonstrate that HQDR achieves consistent gains over strong baselines and exhibits superior robustness when transferring between datasets with distinct structural characteristics.

Question-Answering (QA) systems are vital for rapidly accessing and comprehending information in academic literature.However, some academic questions require synthesizing information across multiple documents. While several prior resources consider multi-document QA, they often do not strictly enforce cross-document synthesis or exploit the explicit inter-paper structure that links sources.To address this, we introduce a pipeline methodology for constructing a Multi-Document Academic QA (MDA-QA) dataset. By both detecting communities based on citation networks and leveraging Large Language Models (LLMs), we were able to form thematically coherent communities and generate QA pairs related to multi-document content automatically.We further develop an automated filtering mechanism to ensure multi-document dependence.Our resulting dataset consists of 6,804 QA pairs and serves as a benchmark for evaluating multi-document retrieval and QA systems.Our experimental results highlight that standard lexical and embedding-based retrieval methods struggle to locate all relevant documents, indicating a persistent gap in multi-document reasoning. We release our dataset and source code for the community.