The policy of Universal Salt Iodisation (USI) could reduce population’s thyroid volume (TVOL) in iodine deficiency areas. Conversely, the improved growth and developmental status of children might increase the TVOL accordingly. Whether the decreased TVOL by USI conceals the increase effect of height and weight on TVOL is unclear. The aim of this study was to analyse the association between height, weight, iodine supplementation and TVOL. Five national Iodine Deficiency Disorder surveys were matched into four pairs according to the purpose of analysis. County-level data of both detected by paired surveys were incorporated; 1:1 random pairing method was used to match counties or individuals. The difference of TVOL between different height, weight, different iodine supplementation measures groups and the association between TVOL and them were studied. The mean height and weight of children aged 8–10 years increased from 129·9 cm and 26·9 kg in 2002 to 136·2 cm and 32·1 kg in 2019, while the median TVOL decreased from 3·10 ml to 2·61 ml. Iodine supplementation measures can affect TVOL; after excluding iodine effects, the median TVOL was increased with the height and weight. On the other side, after excluding the influence of height and weight, the median TVOL remained decreased. Only age, weight and salt iodine were significantly associated with TVOL in multiple linear models. Development of height and weight in children is the evidence of improved nutrition. The decreased TVOL caused by iodised salt measures conceals the increase effect of height and weight on TVOL. Age, weight and salt iodine affect TVOL significantly.