The evidence for a link between sleep duration and cardiovascular risk is accumulating in youths, but no study has yet investigated the relationship between sleep duration and change of cardiac structure. In this study, we recruited 559 youths aged 14-28 years from the cohort of Beijing Child and Adolescent Metabolic Syndrome Study. Questionnaire, color Doppler echocardiography, oral glucose tolerance test and blood biomarkers analyses were performed. We found that sleep duration was negatively correlated with body mass index, waist circumstance, and HbA1c (all P < 0.05), but not with adiponectin and leptin. Meanwhile, participants with shorter sleep duration (≤7 h) had larger interventricular septal diastolic thickness, left ventricular (LV) end-diastolic diameter, LV posterior wall thickness, LV mass (LVM), and LV mass index (LVMI), compared to participants in 7-9 h/night or >9 h/night group. Findings remained significant after adjustment for the major confounding factors (P < 0.05). Multivariate regression modeling revealed that each additional hour of sleep was associated with smaller LVM (β: -3.483, P < 0.0001) and LVMI (β: -0.815, P < 0.0001). Our findings suggest that short sleep has a possible direct effect on cardiac remodeling, occurring already at young ages.