The purpose of the current study was to research the factors influencing thyroid volume (TVOL) in 6–12-year-old children and update the reference values. A cross-sectional study was carried out in iodine-sufficient areas of four provinces in China. Urine, edible salt and drinking water samples were collected from children. Children’s height, weight and TVOL were measured. Ridge regression was used to screen variables for solving the multicollinearity problem. Quantile regression was used to analyse the relationship between the quantiles of TVOL and other variables. In total, 5653 children aged 6–12 years were enrolled in this study, including 2838 boys and 2815 girls. There was no significant difference in TVOL between boys and girls (P > 0·05). Spearman correlation analysis showed that total TVOL was positively correlated with age, height, weight, body surface area (BSA) and BMI, and the correlation coefficients were 0·616, 0·663, 0·669, 0·685 and 0·479, respectively. Among them, the correlation between TVOL and BSA was the strongest. According to the ridge regression results, age and BSA influenced TVOL, and the ridge regression coefficients were 0·13 and 0·94, respectively. Quantile regression further showed that age and BSA had significant influences on the whole TVOL distribution (P < 0·001). Therefore, the TVOL of children aged 6–12 years in China was mainly influenced by age and BSA, and reference values for TVOL of different genders based on age and BSA were established.