The clustering of diet quality, physical activity, and sleep and its association with cardiometabolic risk (CMR) factors remains to be explored. We included 5315 children aged 6–13 years in the analysis. CMR score (CMRS) was computed by summing Z-scores of waist circumference, an average of systolic and diastolic blood pressure, fasting glucose, high-density lipoprotein cholesterol (multiplying by −1), and triglycerides. Low diet quality and low cardiorespiratory fitness (CRF) were more likely to be seen in a pair, but low diet quality was less likely to be clustered with unhealthy sleep patterns. Low diet quality, low CRF, and unhealthy sleep pattern was associated with a 0.63, 0.53, and 0.25 standard deviation (SD) higher increase in CMRS, respectively. Compared to children with no unhealthy factor (−0.79 SD), those with ≥1 unhealthy factor had a higher increase (−0.20 to 0.59 SD) in CMRS. A low diet quality-unhealthy sleep pattern resulted in the highest increase in CMRS, blood pressure, and triglycerides. A low diet quality–low CRF-unhealthy sleep pattern resulted in the highest increase in fatness and fasting glucose. Unhealthy factor cluster patterns are complex; however, their positive associations with changes in CMR factors are consistently significant in children. Some specific patterns are more harmful than others for cardiometabolic health.