Objective: To explore the effect of a preschool-based fluoride application on early childhood caries (ECC) prevention among 5 to 6-years old children in two urban districts of Xi’an. Methods: This cross-sectional study was conducted by using a two-stage cluster method. A total of 564 children aged 5 to 6-years old from eight preschools were recruited for this study. Each participant was assessed dental caries and debris index. Time and materical for topical fluorine application was recorded. Parents/guardians completed a structured self-administered questionnaire, which included demographic, family and social factors (educational level of parents,household monthly income, etc). Children’s oral health related behaviors (age to start brushing, brushing tooth frequency, parents supports in child’s teeth brushing, and whether use fluoride toothpaste); dietary habit (frequency of dessert, desert before sleep, dental discomfort within 12 months, visits to dentist within 12 months). The status of dental caries was shown in the form of the mean dmft and the prevalence of ECC. Results: The prevalence of ECC and mean dmft of children was 63.8% and (3.00±3.33) respectively. Among the 294 children aged 5-6 years old, the average intervention time was (4.83±1.00), 33.7% of the children only applied fluorine vanish, 66.3% of the children applied fluorine vanish and fluorine foam. The prevalence of ECC was 53.5%, 63.1% and 68.1% in the children who applied fluorine vanish, fluorine vanish and fluorinated foam, no fluoride, respectively. The mean dmft was (2.45±3.42)(2.83±3.04) and (3.32±3.47), respectively, with statistically significant differences(χ2/F=6.77, 7.08, P<0.05). According to binary Logistic regression equation analysis, the application of fluorine vanish was negatively associated with the prevealence of ECC(OR<1.00). High frequency of dessert intake, low degree of oral hygiene and late start of brushing teeth was positively associated with deciduous teeth caries(OR>1.00). Negative binomial regression analysis of dmft was independent of local fluoride intervention(P>0.05). Conclusion The effect of preschool-based fluoride intervention to prevent ECC was limited. It is necessary to improve the effect of intervention for children, carry out targeted health education，encourage parents to intervene eating and brushing behavior of children as early as possible.