Against the backdrop of rapid global urbanization, peri-urban villages universally face the dual dilemmas of landscape homogenization and the imbalance between heritage preservation and functional renewal. As a typical representative, the “Shanghai-style Jiangnan” villages feature an open water–land chessboard pattern and linear water-house parallel organization, which are distinctly different from the closed and introverted texture of traditional Suzhou-Hangzhou water towns. Such villages urgently need to balance the continuation of the original spatial fabric and the adaptation of modern functions. Existing studies on rural landscapes mostly focus on the static vertical identification of single elements, lacking a systematic quantitative analysis of the horizontal topological relationships among multiple elements, making it difficult to accurately define the spatial boundaries between preservation and renewal. This study takes Xinyuan Village in Jinshan District, Shanghai, as an empirical subject to construct a model for the vertical gene decoding of the “Point-Line-Network” and horizontal topology coupling of “Surface Gene.” By introducing a landscape sensitivity assessment combined with the Entropy Weight Method (EWM) and GIS (Geographic Information System) spatial Kernel Density Estimation (KDE), a quantifiable landscape control heat map is generated. The study identifies the nested original fabric structure of the “house-water-field-forest-road” and the spatial landscape differentiation characteristics in Xinyuan Village and delineates three-tier differentiated zoning controls through dual-verified heat maps. Validated based on Xinyuan Village, this method effectively resolves the conflict between rural preservation and renewal and realizes the transformation from static museum-style preservation to refined adaptive zoning. It provides specific practical strategies for the renewal of “Shanghai-style Jiangnan” villages and offers a quantitative morphological reference for enhancing the spatial resilience and living heritage of peri-urban villages, while its cross-regional transferability needs further verification.