Objective To analyze the nutritional status and change trend of children under 5 years old in urban and rural areas of Yunnan Province,based on the data of Yunnan Province in nationwide children's Nutrition and Health Condition Monitoring System from 2012 to 2018. Methods A stratified cluster sampling method was used to select children under 5 years old in 4 towns (streets) respectively in Wuhua district,Kunming and Huize district,Qujing. The diagnostic criteria of children's growth development and anemia by WHO in 2006 was adopted. And the data was analyzed by software SPSS 17.0. Results The prevalence of anemia in rural children under 5 years old was over 30% (after high adjustment of altitude),which has become a moderate issue of public health. However,the prevalence of anemia has decreased significantly over the past seven years,with significant difference between urban and rural areas(P＜0.05). Meantime,the prevalence rates of stunting,underweight and wasting in children under 5 years old in rural area were significantly higher than those in urban area(P＜0.05),which significantly changed over the past seven years,especially in rural area(P＜0.05). Conclusions The nutritional disease of children in urban and rural areas of Yunnan province has been alleviated dramatically. The launch of related projects on improving nutritional status of children in poverty areas has enhanced the nutritional status of children in western area,which needs to be implemented thoroughly.