Diet plays a critical role in the development of obesity and obesity-related morbidities. Our study aimed to evaluate the dietary food groups, nutrient intakes and eating behaviors of metabolically healthy and unhealthy obesity phenotypes in an Asian cohort of children and adolescents. Participants (n = 52) were asked to record their diet using a 3-day food diary and intakes were analyzed using a nutrient software. Eating behavior was assessed using a validated questionnaire. Metabolically healthy obesity (MHO) or metabolically unhealthy obesity (MUO) were defined based on criteria of metabolic syndrome. Children/adolescents with MUO consumed fewer whole grains (median: 0.00 (interquartile range: 0.00–0.00 g) vs. 18.5 g (0.00–69.8 g)) and less polyunsaturated fat (6.26% kcal (5.17–7.45% kcal) vs. 6.92% kcal (5.85–9.02% kcal)), and had lower cognitive dietary restraint (15.0 (13.0–17.0) vs. 16.0 (14.0–19.0)) compared to children/adolescents with MHO. Deep fried food, fast food and processed convenience food were positively associated with both systolic (β: 2.84, 95%CI: 0.95–6.62) and diastolic blood pressure (β: 4.83, 95%CI: 0.61–9.04). Higher polyunsaturated fat intake (OR: 0.529, 95%CI: 0.284–0.986) and cognitive dietary restraint (OR: 0.681, 95%CI: 0.472–0.984) were associated with a lower risk of the MUO phenotype. A healthier diet composition and positive eating behavior may contribute to favorable metabolic outcomes in children and adolescents with obesity.