Stone arch bridges represent culturally significant heritage assets that exhibit distinct regional characteristics. At present digital preservation largely attends to geometric modeling and typically neglects the identification and conformance of core culture genes. This oversight has resulted in a disconnect between technological application and core heritage values, a prevalent issue globally. To address this, this study employs cultural gene theory to formulate a systematic framework for investigating the architectural cultural genes of stone arch bridges from the three dimensions: material–morphological, technical–behavioral, and cultural–symbolic. This study takes the Hongji Bridge in Handan as an example and uses literature research and 3D laser scanning and UAV oblique photogrammetry and qualitative extraction and visual presentation of the architectural genetic characteristics of stone arch bridges. This study identifies 11 core genetic indicators from the dimensions of genetic architecture, inheritance, and evolution, for the architectural cultural genes for the Chinese stone arch bridges The Zhaozhou Bridge (China) and Serranos Bridge (Europe)’s cross-cultural comparative analyses are adopted to validate the generalizability of the framework and the genetic uniqueness of the Chinese stone arch bridge. This research introduces a gene-based model of digital conservancy that fosters the transition of heritage preservation from technology-driven to value-driven.