The preschool years are a sensitive period for the development of food preferences that will affect physical growth and life-long health. The promotion of healthy eating and nutritional status was achieved by adapting the US National Aeronautics and Space Administration (NASA) Mission X (MX) Program among young children in South Korea. The intervention program was delivered by nutritional experts and class teachers over 10 weeks. Children from 37 school classes (n = 534) from 7 daycares and kindergartens were randomized into a control group (CG, n = 280) and an intervention group (IG, n = 254). Parents were surveyed for their children’s characteristics and nutrition quotient (NQ) at baseline and at the 10-week follow-up. At baseline, 18.8% (boys: 18.9%; girls: 18.8%) of the subjects were overweight or obese (body mass index ≥ 85th percentile). After the intervention, the mean differences in various anthropometric measures did not differ significantly between the groups in a linear regression model adjusted for age, sex, and type of school. The NQ grades were significantly higher in the IG than the CG after the intervention (p = 0.000). In summary, the 10-week South Korean MX program improved the eating behaviors and nutrition status of young children. A further multisector prevention program is needed to prevent childhood obesity in young children.