Documentary heritage constitutes a crucial witness to the Silk Road, underpinning the cultural foundation of the Belt and Road Initiative. Despite mature preservation mechanisms, there exists an imbalance between micro-level semantic analysis and macro-level cultural interpretation. To bridge this gap, the study proposes an underlying logic for decoding and translating cultural genes in China’s overland Silk Road heritage, and develops a three-stage framework based on semantic expression, associative aggregation, and scenario reconstruction. Using Zhang Qian’s missions to the Western Regions as a case, the research constructs a multi-layered semantic system from 273 data objects, encompassing resource, knowledge, and service layers. The results demonstrate how cultural genes embedded in documentary heritage can be systematically identified, semantically linked, and digitally activated, offering a novel perspective for understanding the cultural evolution of the Silk Road.