We examined the temporal changes in obesity and sleep habits and their relationship in a prospective cohort of healthy Chinese adolescents. We collected data on anthropometric and questionnaire-measured sleep parameters in 2007-2008. 516 participants returned for examinations in 2013-2015. General obesity was defined as body mass index (BMI) ≥age- and sex-specific 95th percentile or ≥25 kg/m2 for participants aged <18 or ≥18 years, respectively. Central obesity was defined as waist circumference (WC) ≥ age- and sex-specific 90th percentile or using adult cut-offs. After a mean follow-up of 6.2 ± 0.5 years, the mean BMI increased from 18.5 ± 3.1 to 20.9 ± 3.4 kg/m2. The corresponding WC were 63.7 ± 8.9 and 69.8 ± 9.7 cm. General obesity rate increased from 8.3% (95% confidence interval [CI] 6.1-11.1) to 11.3% (8.7-14.4; p = 0.034). Central obesity rate decreased from 16.9% (13.7-20.4) to 13.5% (10.6-16.8; p = 0.034). During follow-up, more participants reported short sleep (<7 hours/day during weekday: 20.5% [17.1-24.2] vs. 15.3% [12.3-18.8]; p = 0.033) and bedtime after midnight (60.5% [56.2-64.8] vs. 16.2% [13.1-19.7]; p < 0.001) than baseline. The relative risk of overweight/obesity in participants with short sleep and late bedtime was 1.30 (0.48-3.47) and 1.46 (0.70-3.05), respectively. Despite rising rates of unhealthy sleep habits and general obesity, their associations were not significant at 6-year of follow-up.