Objectives: Prior evidence suggests geographic disparities in the effect of maternal education on child nutritional status between countries, between regions and between urban and rural areas. We postulated its effect would also vary by micro-geographic locations (indicated by mountain areas, plain areas and the edge areas) in a Chinese minority area. Methods: A cross-sectional study was conducted with a multistage random sample of 1474 school children aged 5-12 years in Guyuan, China. Child nutritional status was measured by height-for-age z scores (HAZ). Linear mixed models were used to examine its association with place of residence and maternal education. Results: Micro-geographic disparities in child nutritional status and the level of socioeconomic composition were found. Children living in mountain areas had poorer nutritional status, even after adjusting for demographic (plain versus mountain, β = 0.16, P = 0.033; edge versus mountain, β = 0.29, P = 0.002) and socioeconomic factors (plain versus mountain, β = 0.12, P = 0.137; edge versus mountain, β = 0.25, P = 0.009). The disparities significantly widened with increasing years of mothers' schooling (maternal education*plain versus mountain: β = 0.06, P = 0.007; maternal education*edge versus mountain: β = 0.07, P = 0.005). Moreover, the association between maternal education and child nutrition was negative (β = - 0.03, P = 0.056) in mountain areas but positive in plain areas (β = 0.02, P = 0.094) or in the edge areas (β = 0.04, P = 0.055). Conclusions: Micro-geographic disparities in child nutritional status increase with increasing level of maternal education and the effect of maternal education varies by micro-geographic locations, which exacerbates child health inequity. Educating rural girls alone is not sufficient; improving unfavorable conditions in mountain areas might make such investments more effective in promoting child health. Nutrition programs targeting to the least educated groups in plain and in edge areas would be critical to their cost-effectiveness.