BACKGROUND Great growth inequalities between urban and rural areas have been reported in China over the past years. By examining urban/rural inequalities in physical growth among children < 7 years old over the past three decades from 1985 to 2015 in Guangzhou, we analyzed altering trends of anthropometric data in children and their association with economic development during the period of rapid urbanization in Guangzhou. METHODS The height, body weight and nutrition status of children under 7 years old were obtained from two successive cross-sectional surveys and one health surveillance system. Student's t-test, Spearman's rank-order correlation and polynomial regression were used to assess the difference in physical growth between children in urban and rural areas and the association between socioeconomic index and secular growth changes. RESULTS A height and weight difference was found between urban and rural children aged 0-6 years during the first two decades of our research (1985-2005), which gradually narrowed in both sex groups over time. By the end of 2015, elder boys (age group ≥5 year) and girls (age group ≥4 year) in rural areas were taller than their counterparts in urban areas (p < 0.05).The same trend could be witnessed in the weight of children aged 6 years, with a - 1.30 kg difference (P = 0.03) for boys, and a - 0.05 difference (P = 0.82) for girls. When GDP increased, the gap in boys' weight-for-age z-score (WAZ from 0.25 to 0.01) and height-for-age z-score (HAZ from 0.55 to 0.03) between urban and rural areas diminished, and disappeared when the GDP per capita (USD) approached 25,000. In either urban or rural areas, the urbanization rate and GDP were positively associated with the prevalence of obesity (all R > 0.90 with P < 0.05) and negatively correlated with the prevalence of stunted growth (all R < -0.87 with P < 0.05). CONCLUSIONS Growth inequalities gradually decreased with economic development and urbanization, while new challenges such as obesity emerged. To eliminate health problems due to catch-up growth among rural children, comprehensive intervention programs for early child growth should be promoted in rural areas.