Objective To investigate the content and changes of fluoride in corn and pepper, to evaluate the effect of prevention and control measures, and to provide a basis for adjusting the prevention and control strategy. Methods In 2013, according to the different directions of east, west, south, north and center, 5 townships were selected from each coal-burning-borne endemic fluorosis areas in all 23 counties (cities, districts), and 3 villages was randomly selected from each township. Household samples of corn and dried pepper in 10 households were collected to detect fluorine content. The results of 14 counties were compared with the 2007 survey data. Results A total of 884 and 3379 samples of corn and pepper were collected, and the median fluorine content was 1.26 and 9.15 mg/kg, the range was 0.50~254.59 mg/kg and 0.50~3701.88 mg/kg, respectively. Compared with the survey data of 2007, the median fluoride content of corn of 14 counties decreased by nearly 50%, and the median amount of pepper was reduced by more than 80%. The differences were statistically significant (mg/kg:corn 1.36 vs 2.63, dried pepper 9.70 vs 55.31, Z = 3.28, 9.13, P<0.05). Conclusion The fluoride content of corn and pepper in Guizhou Province is significantly lower, but it is still relatively high in some coal-burning-borne fluorosis counties (cities, districts).