In the coal-burning fluorosis areas of China, over 10 million people suffer from dental fluorosis caused by multiple pathways of fluoride intake. However, the link between dental fluorosis prevalence, the geochemical distribution of fluoride, and contributions of different exposure pathways remain unclear. Here, we aimed to quantify the various fluoride exposure pathways and establish the association between dental fluorosis and fluoride intake in Southwest China. Epidemiological data on the peak time of fluorosis prevalence were combined with geochemical analyses of the fluoride content in coal and clay over a large scale, the amounts and ratios of fluoride intake through different exposure pathways were calculated, and the association between the total daily fluoride intake (TDFI) and dental fluorosis severity was analyzed. The prevalence of dental fluorosis was not significantly correlated with the fluoride geo-background of coal and clay on a large scale (P > 0.05). The co-combustion of coal and clay contained in hand-made briquettes is the main pathway of fluoride contamination, which occurs through the inhalation of polluted air and consumption of contaminated roasted products. Furthermore, the TDFI per person ranged from 2.78 to 17.32 mg, and it was significantly positively correlated with the prevalence of dental fluorosis (P < 0.05). The TDFI from breathing and eating was 1.1–3.2 mg and 1.1–15.1 mg, which accounted for 9%–54% and 40%–90% of the total TDFI, respectively. The combination of living habits and soil geochemical fluoride anomalies resulted in the higher prevalence of fluorosis in rural areas of Southwest China.