As a vital cradle of Chinese civilization, the Yangtze River Basin possesses a wealth of ancient architectural heritage that serves as a material record of civilizational evolution. This study takes 688 nationally protected ancient architectural sites within the 11 provincial-level administrative regions along the main stream of the Yangtze River as its research objects. Utilizing GIS platforms and methods including the Nearest Neighbor Index, Kernel Density Estimation, Standard Deviational Ellipse, and Imbalance Index, we systematically analyze their spatio-temporal distribution characteristics. The results indicate the following: (1) Spatially, the ancient architecture exhibits a pattern of “multi-center agglomeration and axial diffusion,” with an overall clustered distribution, forming a dual-core structure with the Jiangsu–Anhui region in the lower reaches as the primary core and the Sichuan Basin in the upper reaches as the secondary core. (2) A quantitative temporal profile of the extant heritage was established, revealing a pronounced pyramid-shaped structure dominated by Ming–Qing (74.56%) and Song-Yuan (18.60%) remnants. Beyond merely reflecting material durability, this profile is shown to be a legacy of historical construction peaks driven by technological standardization and macro-economic shifts, which fundamentally preconditioned the spatial patterns analyzed. (3) The spatio-temporal evolutionary trajectory follows a path from “marginal aggregation” during the Sui, Tang, and Five Dynasties, to the establishment of a “dual-core structure” in the Song–Yuan periods, and finally to “axial diffusion” in the Ming–Qing periods. This study constructs a geographic analysis framework for cultural heritage at the basin scale, and its findings can inform the planning of heritage corridors and provide a reference for regional conservation strategies.
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