The spatiotemporal distribution characteristics of cultural heritage reveal the trajectory of human activity changes, and a deep analysis of its natural and cultural factors holds significant reference value for the overall conservation and management of cultural heritages. This study focuses on the cultural heritage at the provincial level and above in Fujian, utilizing GIS spatial analysis to explore the spatiotemporal evolution of cultural heritages and their natural and human influencing factors. The research findings are as follows: (1) The distribution of cultural heritage in Fujian exhibits a clustering pattern, with dense areas transitioning from the upstream regions of the prehistoric and pre-Qin periods to the eastern coastal areas gradually. (2) The Ming and Qing dynasties have the highest number of cultural heritages, with the type of heritage transitioning from ancient sites in the early periods to ancient architecture, and in modern times, mainly important historical sites and representative architectural heritages. (3) The overall centroid coordinates of cultural heritage reveal a shift from the northern part of Fujian to the eastern and southern parts. (4) Natural factors significantly influence the distribution of cultural heritage, with a higher concentration in plain and hilly areas, on slight slopes with gradients between 0.5° and 2.0°, and on the southern and southeastern slopes, especially within a 1-kilometer radius of rivers. (5) The creation of cultural heritage during historical periods is closely linked to the regional history, culture, political, and economic environments. The positive development of these socio-cultural factors has a promotional effect on the quantity of cultural heritage. This study demonstrates the utility and applicability of GIS spatial analysis techniques in cultural heritage research, providing a methodological framework that can be adapted and applied internationally. The findings offer insightful data that can inform targeted conservation and development strategies for cultural heritage, ensuring their effective preservation and sustainable management across different regions.