The aim of this study was to determine how malnutrition rates change in young Chinese children when 2006 World Health Organization (WHO) growth standards are used instead of 1978 WHO/National Center for Health Statistics reference. Cross-sectional survey data were used from rural western China and the Tibet region. The heights and weights of children of <36 months of age were measured. The nutritional status of the children was assessed by two references. Using 2006 reference instead of 1978 reference, the prevalence of stunting increased significantly (17.9% vs. 12.3% in rural western China and 37.5% vs. 28.1% in rural Tibet). The prevalence of underweight was lower in rural western China (7.7% vs. 11.7%) than rural Tibet (13.1% vs. 15.3%). For all ages, the prevalence of stunting increased and the greatest relative increase appeared in the first six months (102.9% in rural western China vs. 134.9% in rural Tibet). With respect to underweight, the relative increase occurred only during the first six months (314.3% in rural western China vs. 48.1% in rural Tibet); however, the reduction was observed in other age groups. For young Chinese Han and Tibetan children, the difference in estimation of malnutrition between two references differed in magnitude. The scale of change in the prevalence rates of stunting and underweight is much greater when 2006 reference was introduced.