Abstract: Against the backdrop of protecting and inheriting rural characteristics at the grassroots level under the strategy of rural revitalization, this paper addresses the inadequacies in research regarding the evolutionary process and influencing mechanisms within the field of rural characteristics studies. It introduces the theory of spatial genes, with a focus on Bishan District, a rural area characterized by unique features in western Chongqing. By adopting the technical pathway of 'scene-feature-gene' the paper reverses the decoding process to identify and extract four major spatial genes in rural settlements in western Chongqing: 'ringed hills', 'pond-adjacent', 'freely scattered in a discontinuous bead-like pattern', and 'open courtyards stacked in a simple and unsophisticated manner'. Building upon this foundation, the paper delves into the historical evolution process and patterns of these spatial genes. Utilizing technical means such as historical document mining, image restoration, remote sensing interpretation, and empirical fieldwork research, it systematically reviews the scene characteristics and feature factors of these spatial genes across different historical periods, ranging from the Ming and Qing dynasties to the contemporary era. Based on the dual dimensions of natural environment and socio-culture, the paper analyzes the diachronic (over time) and synchronic (at the same time) spatio-temporal characteristics of the evolution of these spatial genes. Furthermore, it employs the Analytic Hierarchy Process (AHP) to quantitatively evaluate the weights of nine categories of influencing factors across three levels, thereby revealing the complex mechanism of multidimensional element layering and mutual influence exhibited by spatial genes in the process of environmental inheritance and evolution. This provides theoretical and technical support for the protection and inheritance of characteristic genes in rural areas at the grassroots level.