To explore the prevalence of and risk factors for glycolipid metabolism disorder (GLMD) from the prenatal period through childhood and adolescence. A bidirectional cohort study which was established in 2014 and followed between March 1 and July 20, 2019 were designed to evaluate the risk factors for GLMD. Two stage stratified cluster sampling was used to include participants from four communities in two counties in Chongqing. 2808 healthy children aged between 6 and 9 years in 2014 entered the cohort in 2014, and followed in 2019 with a follow-up rate of 70%. 2,136 samples (aged 11·68 ± 0·60 years) were included. The prevalence of insulin resistance (IR), prediabetes/diabetes and dyslipidemia was 21·02%, 7·19% and 21·61%, respectively. Subjects with an urban residence, no pubertal development, dyslipidemia in 2014, higher family income, higher parental education, low quality of life (QoL), and unstable neurotic and psychotic personalities had significantly elevated fasting insulin (FI) or homeostasis model assessment insulin resistance (HOMA-IR) levels; subjects with female sex, no pubertal development, dyslipidemia in 2014, obesity, gestational hypertension, maternal weight gain above Institute of Medicine guidelines, single parents, low QoL, introverted and unstable personality had increased triglyceride or triglyceride/high-density lipoprotein (HDL). Adolescent with rural residence and living convenience had higher HbA1c level. We observed that low QoL status, unstable and psychotic personality traits were associated with increased GLMD risk independent of obesity, suggesting that the community intervention to improve the QoL and psychological health of children is essential.