Objectives To compare the difference between the China growth reference and the WHO growth standards in assessing malnutrition of children under 5 years.

Settings The households selected from 31 provinces, autonomous regions and municipalities in mainland China (except Taiwan, Hong Kong and Macao).

Participants Households were selected by using a stratified, multistage probability cluster sampling. Children under 5 years of age in the selected households were recruited (n=15 886).

Primary and secondary outcome measures Underweight, stunting, wasting, overweight and obesity.

Results According to the China growth reference, the prevalence of underweight (8.7% vs 4.8%), stunting (17.2% vs 16.1%) and wasting (4.4% vs 3%) was significantly higher than that based on the WHO growth standards, respectively (p<0.001); the prevalence of overweight was lower than that based on the WHO growth standards (9.4% vs 10.2%, p<0.001). In most cases, the prevalence of undernutrition assessed by using the China growth reference was significantly higher. However, the prevalence of overweight was significantly lower by using China charts for boys aged 3–4, 6, 8, 10, 12–18 and 24 months.

Conclusions The WHO growth standards could be more conservative in undernutrition estimation and more applicable for international comparison for Chinese children. Future researches are warranted for using the WHO growth standards within those countries with local growth charts when there are distinct differences between the two.