Parsing visual documents into machine-readable representations is fundamental to document intelligence. Existing benchmarks focus on page-level element recognition, reading order, formula recognition, and table structure. Long documents, however, also require document-level structure recovery. This includes reconstructing cross-page table-of-contents (TOC) hierarchies and identifying typed links from tables and figures to their captions, notes, and sources, often in one-to-many form. Because these structures are covered only partially or subsumed within broader parsing protocols, existing benchmarks cannot directly evaluate two key document-level tasks: \emph{Table-of-Contents Hierarchy Recovery} and \emph{Contextual Relationship Recovery}. To benchmark these two tasks, we introduce \textsc{LongDocBench}, comprising 85 real-world financial reports, textbooks, and academic papers spanning 2,582 pages, with up to 105 pages per document. It provides human-verified annotations for 3,937 heading nodes (mean node depth 3.55; maximum depth 9) and 3,258 contextual relationships annotated across 2,680 table and figure objects. We further evaluate both the downstream utility and recoverability of these structures. Long-document question-answering experiments show that human-verified TOC hierarchies and contextual relationships improve reasoning, with their combination providing complementary benefits. Meanwhile, representative document parsers remain limited on both recovery tasks despite strong page-level performance. To support further progress, we publicly release \textsc{LongDocBench} and its evaluation protocol and reproducible testbed for advancing document-level structure recovery in long documents.
RAG systems rely on chunking, which destroys structural information in documents. Existing heading-based retrieval (Jeong et al., 2025) requires multiple LLM calls per document and returns sub-chunks within matched sections. We introduce ToC-guided page retrieval, which infers headings from visual formatting without LLM calls, embeds them as a parallel index, and loads full page sections. Across 1,280 conditions on 8 enterprise documents (5 to 195 pages), we find: (1) ToC is a significant main effect on answer quality (d = +0.41, p = 0.031), with the largest gains in completeness (+0.40) and usefulness (+0.40); (2) combined with answer-side verification, it outperforms query-side decomposition + verification (d = +0.32, p = 0.036); (3) ToC contributes 20% of citations despite adding only 2.9 pages per query; (4) gains are directionally larger on longer documents (up to +1.50 on 118 pages), though the trend does not reach significance with 8 documents; and (5) a 480-condition sensitivity analysis finds no significant parameter effects (all p > 0.38), confirming defaults are near-optimal. The contribution is both methodological (a new zero-LLM-cost retrieval algorithm) and empirical: factorial evidence that document-side, query-side, and answer-side enhancements are complementary, a three-way interaction not previously studied.