China’s northern Fujian, as one of the spatial carriers of renowned traditional Chinese cultures such as Minyue, Zhu Xi’s Neo-Confucianism, tea, and porcelain, has preserved a wealth of tangible cultural relics, showcasing a profound cultural heritage and possessing strong research value and development potential. This study employs GIS spatial statistical analysis and map visualization technology to unveil the evolutionary processes of cultural heritage sites in northern Fujian, focusing on their spatial types, forms, and densities across different historical periods. Based on this foundation, the research further delves into the intrinsic relationships between the spatial distribution characteristics of cultural heritage sites in northern Fujian during various historical periods and the local natural and cultural environment. The results indicate that: (1) the spatial distribution of cultural heritage sites in northern Fujian varies across different historical periods, with the highest concentration and quantity observed during the Ming and Qing periods. In contrast, the Qin, Han, Wei, Jin, Northern and Southern Dynasties period exhibits the lowest quantity and a more dispersed distribution. (2) Cultural heritage sites in northern Fujian are mainly distributed in the relatively flat terrain below 400 m above sea level, including middle to low-altitude mountain basins, river valleys, and low hills. In terms of distance from rivers, cultural heritage sites exhibit a clear distribution pattern along rivers, with a large number of them located within 0–6 km from the riverbanks. (3) The spatial distribution of cultural heritage sites in northern Fujian is influenced not only by macro-environmental factors such as topography, altitude, and rivers but also by micro-shaping from social and cultural elements like Minyue culture, tea and porcelain ancient road culture, Zhu Xi’s Neo-Confucianism culture, religious beliefs and customs culture, and red revolutionary culture across different historical periods. This study contributes to the establishment of a model correlating cultural heritage sites with historical periods and provides an interdisciplinary methodological framework to understand the relationship between cultural heritage sites and the geographical environment.