<jats:p>We examined whether energy and macronutrient intake from different meals was associated with changes in cardiometabolic risk (CMR) factors in children. CMR score (CMRS) was computed by summing Z-scores of waist circumference, the average of systolic and diastolic blood pressure, fasting glucose, high-density lipoprotein cholesterol (multiplying by −1), and triglycerides. We included 5517 children aged 6–13 years from six major cities in China. Five meal patterns were identified according to energy intake: balanced, breakfast dominant, lunch dominant, dinner dominant, and snack dominant patterns. These patterns were not significantly associated with changes in CMR factors. Carbohydrate intake (% energy) at lunch was positively associated with the change in CMRS (beta coefficient (95% CI): (0.777 (0.509, 1.046) in quintile 5 versus quintile 1). A positive association between carbohydrate intake at dinner and change in CMRS was observed. High protein intake at both lunch and dinner was associated with a favorable change in CMRS. Moderate fat intake at lunch was associated with a lower increase in CMRS. Meal patterns driven by energy were not significantly associated with CMR factors; however, a low carbohydrate-high protein-moderate fat lunch and low carbohydrate-high protein dinner were associated with favorable changes in CMRS in children.</jats:p>