Background: Early childhood obesity is highly associated with obesity in adolescents and adults. However, studies on specific eating behaviors that have a decisive effect on obesity in early childhood (aged 3–5 years) are scarce. We hypothesized that critical risk factors associated with eating behaviors leading to obesity at ages of 3–5 years may be different. To confirm this hypothesis, we conducted a study on the risk factors of obesity related to eating behaviors in preschool children. Methods: Using the National Health Screening Program for Infants and Children (NHSPIC) in Korea’s general population cohort, we found the obesity trends in 3–5-year-olds. The risk factors of obesity in 3–5-year-olds were analyzed through logistic regression. Results: Among children with obesity at 3 years old, but without obesity at 4 years old, only 10.1% (107/1063) transitioned to obesity at 5 years old, whereas among children with obesity at 3–4 years old, 62.7% (398/635) transitioned to obesity at 5 years old. The risk factors for obesity at 3 years old were inclusion of meat in complementary food, prolonged breastfeeding, and consumption of sweetened beverages; at ages 4–5 years, the risk factors were the inclusion of meat in complementary food and consumption of sweetened beverages. Conclusions: Obesity at 4 years is more likely to lead to obesity in the following year than obesity at 3 years. The dietary factor with the greatest impact on obesity in children aged 3–5 years has been found to be consumption of sweetened beverages.