Adopting a genetic perspective and based on a GIS platform, this study integrates methods such as kernel density estimation, street distribution density analysis, bivariate spatial autocorrelation, and mean center analysis to investigate the formative processes and driving mechanisms behind the growth of guild halls in the Old City of Beijing during the Ming, Qing, and Republican periods. The findings reveal that: 1) The Ming dynasty represented the embryonic stage of guild hall development, the Qing dynasty the flourishing stage, and the Republican period the declining stage. 2) Guild halls were mostly established in areas characterized by concentrated literati activities, prosperous commerce, and frequent population mobility, with the highest concentrations observed in the Xianyukou area near Qianmen in the Ming dynasty, the Fayuan Temple area in Xuannan during the Qing dynasty, and the western Inner City during the Republican period. 3) New guild halls were mostly located along major streets or alleys close to main streets or waterways, with high concentrations in Gaomiao Hutong during the Ming dynasty, Chengxiang Hutong during the Qing dynasty, and Chenggen West Street and North Street in the Inner City during the Republican period. 4) There was a significant spatial correlation between the distribution of newly established literati guild halls and commercial guild halls during the Ming and Qing periods. Three types of clustering—high-high, high-low, and low-high—were observed. In the Ming dynasty, both types of guild halls formed a high-high cluster to the south of Zhengyangmen Gate while simultaneously spreading out to form high-low and low-high clusters. In the Qing dynasty, the high-high cluster expanded from Xianyukou, accompanied by the growth of high-low and low-high clusters. 5) The spatial center of guild halls shifted overall from east to west and from south to north. The migration pattern of literati guild hall centers aligned closely with the overall trend, while the centers of commercial guild halls moved only within the Qianmen area. 6) Four major factors, namely institutional policy, commodity economy, population mobility, and urban construction, interacted to shape the growth process and the cultural rise and decline of Beijing’s guild halls. These findings deepen the understanding of the stage-based dynamic evolution of the city’s historical spatial structure and highlight the potential of GIS for refined research on historic urban areas.