The microbial composition of dental caries may depend on age, diet, and geography, yet the effect of geography on these microbiomes is largely underexplored. Here, we profiled and compared saliva microbiota from 130 individuals aged 6 to 8 years old, representing both healthy children (H) and children with severe caries (C) from two geographical regions of China: Qingdao Guangzhou. First, the saliva microbiota exhibited profound differences in diversity and composition between the C and H groups. The caries microbiota featured a lower alpha diversity and more variable community structure than the healthy microbiota. Furthermore, the relative abundance of several genera (e.g., Lactobacillus, Gemella and Cryptobacterium) was significantly higher in the C group than in the H group. Next, geography dominated over disease status in shaping salivary microbiota, and a wide array of salivary bacteria was highly predictive of the individuals’ city of origin. Finally, we built a universal diagnostic model based on 14 bacterial species, which can diagnose caries with 87% and 85% accuracy within each city and 83% accuracy across cities. These findings demonstrated that despite the large effect size of geography, a universal model based on salivary microbiota has the potential to diagnose caries across human populations.