Obesity and early childhood caries are two prominent health problems affecting the majority of children worldwide. Thus, early childhood caries in obese children must be studied. This study was conducted to investigate the status of early childhood caries in obese children in Hanoi, Vietnam, and its associated factors. A cross-sectional study was conducted on 234 obese children, 234 normal children (non-obese) aged 36 to 71 months, and their mothers at some kindergartens in Hanoi. Study subjects were randomly selected with similarities in age, gender, and study location. Decayed tooth of children was detected by clinical examination and Diagnodent Kavo 2190 machine of Germany. In addition, a questionnaire for their mothers was used to find out related factors. We found that, in the Obese Group, the rate of early childhood caries (ECC), severe-early childhood caries (S-ECC), dmft index (the number of decayed teeth, teeth lost due to cavities, filled decayed teeth or filled cavity), and dmfs index (the number of surfaces of the teeth decay, surfaces of teeth were lost due to cavities, surfaces of filled decayed teeth) were 82.91%, 59.83%, 6.84 ± 4.92, and 9.10 ± 7.48, respectively. In the Normal Group, these rates were smaller than in the Obese Group, but the difference was not statistically significant. Regarding related factors, the hobby of drinking soft drinks, the habits and frequency of drinking milk at night and eating sweet marshmallows were associated with ECC in the Obese Group with p < 0.05. In conclusion, the higher rates of ECC were seen in obese children, with eating hobbies and habits being the related factors. Therefore, it is necessary to have appropriate policies and effective communication strategies to minimize ECC in the future.