This study examined the dietary habits and nutrition quotient (NQ) scores according to leftover food during school meal services among middle school students in the Gyeonggi region. A survey on the dietary habits was conducted among 405 male and female middle school students located in Seongnam City, Gyeonggi Province. The amount of leftover food in the school meals was surveyed using the visual method through a questionnaire over two days. The survey was conducted from July 8, 2019, to July 12, 2019. After calculating the average total leftovers of each student over the two days, they were categorized into the following three groups: the top third was the large leftover group. The middle third was the medium leftover group, and the lower third was the small leftover group. The characteristics of the groups that had leftovers were analyzed. Female, normal-weight, and underweight students accounted for a greater proportion of the large leftover group than male, overweight, and obese students. The rates of selective eating and compliance with new food intake were significantly lower in the large leftover group than in the small leftover group. A comparison of the nutrition quotient for the adolescent (NQ-A) scores of each group revealed significantly lower scores of the large leftover group for all factors (balance, moderation, food diversity, practice, and environment) than the small leftover group. Therefore, there are statistically significant differences in the dietary habits, nutritional quality, and eating behaviors of middle school students that are associated with the amount of leftover food during school meals.