To analyze the influential factors of stunting among children under 7 years of age in nine cities of China in order to provide empirical data for early prevention and intervention for stunting. The survey was carried out with 1∶1 case-control study design in the communities and kindergartens of nine cities (Beijing, Harbin, Xi'an, Shanghai, Nanjing, Wuhan, Guangzhou, Fuzhou, and Kunming) from June to November in 2016. Children of heights lower than the 3 percentile according to the 2009 children's height standard in China were included as the stunting case group (=1 281), and those with normal height matched for geolocation, gender, and age were recruited as the control group (=1 281). The height and weight were measured on site, and the information related to family, perinatal status, diet and feeding, lifestyle, and medical history was collected by questionnaire. Continuous variables were compared by paired samples test and Wilcoxon matched-pair signed ranks test, and proportions were compared by paired Chi square test. Multivariate analysis were carried out using conditional Logistic regression model. Among 1 281 pairs of stunting and control group, there were 677 pairs of boys and 604 pairs of girls, with 238 pairs of children under age 3 years and 1 043 pairs of children aged 3 to 7 years. The Z scores for height and weight of stunting group were lower than that of control group (-2.27 (-2.54, -2.08) -0.59 (-1.04, -0.10), -1.85 (-2.35, -1.38) -0.69 (-1.20, -0.21), =30.982, 25.580, both <0.01). Among family related factors, parental education level, height, weight, and height of grandparents in stunting children were all lower than those in control group (all <0.05). Among individual related factors, proportion of preterm birth, low birth weight, shorter birth length, mother's pregnancy complications, difficulties adding milk or complementary feeding, poor appetite, slow eating, picky and partial eating, passive eating, more snack intake, shorter sleep duration, difficulty falling asleep, disturbed sleep, and recurrent infectious diseases in infant in stunting children were all higher than those in control group (all <0.05). Multivariate Logistic regression analysis results illustrate that the lower the parental education level and the parental height, the higher the risk of stunting. For example, the risk of stunting in children whose fathers had short stature was 6.46 times (95%: 2.73-15.30) of those children whose fathers' height were medium and the risk of stunting in children whose mothers were short stature was 10.56 times (95%: 4.92-22.69) of those children whose mothers' height were medium. The risks of stunting increase significantly among preterm children or those with low birth weight (=2.27, 95%: 1.33-3.88), birth length<45 cm (=3.56, 95%: 1.41-8.98), difficulties adding milk or complementary feeding (=2.04, 95%: 1.32-3.15), poor appetite (=3.20, 95%: 1.74-5.89), slow eating (=1.85, 95%: 1.31-2.63), and food allergy (=1.80, 95%: 1.02-3.16). Parental short stature, preterm birth or low birth weight, shorter birth length, feeding difficulty in infant, poor appetite, slow eating, and food allergy are the main risk factors for stunting in infants and children.