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Background The aim of this study is to explore the spatial heterogeneity of the retention of PFS in children aged 7–9 years in Shanxi Province, North China and investigate the risk factors associated with PFS retention. Methods In this study, 937 children aged 7–9 years from Shanxi Province, China were randomly selected, all of whom had at least one first permanent tooth sealed with PFS in 2016. The children were surveyed after 12 months (in 2017) and 24 months (in 2018). The Geo-detector model was used to explore the spatial heterogeneity of the retention rate of PFS and analyze the influence and interactions of the ecological factors on PFS. Results 3299 teeth from 937 children were analyzed. The PFS full retention rates after 12 months (in 2017) and 24 months (in 2018) were 81.6% and 75.1%, respectively. The incidence of caries of the first molar was 2.1% after 12 months and 5.4% after 24 months. The spatial heterogeneity of the PFS retention rate after 24 months was significant, which was shown as the retention rate of PFS increased from north to south after 24 months. Remarkably, the natural environmental factors exerted greater influence than the socioeconomic and medical resources factors after 12 months, where the interaction of fluorine in water (FW) had the strongest explanatory power of 52% (P P Conclusion The natural environmental factors and medical resources factors are important ecological factors determining the spatial pattern. The government should strengthen medical and technician construction in North China, comprehensively control fluoride in water, optimize the allocation of medical resources, and promote the balanced development of regional medicine.