Objective: To investigate the nutritional status and associated factors of vitamin D among children aged 0 to 12 years old in Chongqing. Methods: From January 2019 to December 2021, 1 877 children aged 0-6 years who received regular child health care were randomly selected from Chongqing maternal and child health hospital, and 707 school age children were also selected from three primary school in Chongqing for investigation. The serum sample were collected for detecting serum 25 (OH) D level by chemiluminescence method, and the possible influencing factors of vitamin D deficiency (VDD) were analyzed. Results: The average serum 25 (OH) D concentration of children was (39.9±9.1) ng/mL with the positive rate of VDD was 14.59%. There were significant differences of VDD positive rate in different age, visiting time, visiting season, body shape, outdoor activity time and vitamin D supplementation (0-3 years old vs 4-6 years old vs 7-12 years old: 14.73% vs 22.19% vs 10.47%; visiting season: spring vs summer vs autumn vs winter: 12.97% vs 10.65% vs 14.86% vs 21.33%; pre COVID 19 epidemic vs post COVID-19 epidemic: 11.18% vs 17.08%; underweight or normal vs overweight or obesity: 12.34% vs 26.13%; adequate outdoor activity time vs inadequate:11.84% vs 16.27%; regular vitamin D supplementation vs irregular vitamin D supplementation: 11.71% vs 15.62% )( χ 2=26.17, 17.59, 30.98, 53.74, 9.60, 6.17, P <0.05). Underweight or normal body weight, sufficient outdoor activities and regular vitamin D supplementation were associated with less vitamin D deficiency with OR(OR95%CI ) at 0.68(0.55-0.84), 0.57 (0.25-0.77) and 0.62(0.44-0.85)( P <0.05). Conclusion The prevalence of VDD among preschool and school age children is high in Chongqing. Integrated prevention and control strategies incluing overweight or obesity control, increasing outdoor activities and oral vitamin D supplements should be taken.