Few longitudinal studies have evaluated the association between eating and drinking habits and the risk of obesity. Therefore, we conducted a 5-year longitudinal big data analysis for evaluating various eating and drinking habits and the risk of obesity. We analyzed individuals without obesity who received medical check-up from 2008 to 2012 and 5 years later from the JMDC Health check-up database. The primary outcome was the incidence of obesity (Body mass index ≥25 kg/m2) and the secondary outcome was the incidence of abdominal obesity (waist circumference ≥85 cm for men and 90 cm for women). Age and sex adjusted, and multivariate logistic regression analyses were conducted. Of 123 182 individuals without obesity at baseline, the median (interquartile range) age was 45 (40, 51) years and 76965 (62.5%) were men. After 5 years, 7133 (5.8%) people developed obesity and 12 725 (10.3%) people developed abdominal obesity. Among six eating and drinking habits, skipping breakfast was associated with a higher risk of obesity (odds ratio [OR], 1.21; 99% confidence interval [CI], 1.10–1.34). In contrast, occasional (OR, 0.86; 99% CI, 0.78–0.94) or daily (OR, 0.79; 95% CI, 0.68–0.91) drinking of alcoholic beverages was associated with a lower risk of obesity. According to the 5-year longitudinal data, eating and drinking habits such as mild to moderate alcohol consumption and avoiding skipping breakfast may result in better obesity prevention. However, excess alcohol consumption would be harmful and should be avoided.