Children’s lung function is a significant predictor of health status throughout their lifetime. This study aims to identify the prevalence of impaired lung function in children and the potential influencing factors in elementary school children of Wuhan, China. Children of 6–12 years old were enrolled from elementary schools in Wuhan, China, in 2018, on the basis of a cross-sectional study design. Information on personal behavior patterns and household characteristics, as well as parental factors, was collected based on a questionnaire survey. Spirometry was used to measure fifteen lung function indicators. Logistic regression models were used to estimate odds ratios of prevalence of impaired lung function with regard to socioeconomic, personal behavior patterns, household, and parental factors, respectively. Four lung function indicators such as FET and EVC in urban children had higher values than in the suburban children after adjusting for confounders (p < 0.05). A higher prevalence of impaired lung function (FEV6, FEV3, EVC, and VC) was found in the children from the rural area than in those from the urban area. A sex difference in FET impairment was observed, however, no significant difference in impairment in other lung function indicators were found between girls and boys. The elevated height and weight of the children was significantly associated with an increased and decreased prevalence of impaired lung function, respectively, particularly both for FEV6, FEV3, FIVC, and FIV1. Opening windows for a longer time in summer was significantly associated with a lower prevalence of impaired FEF25 and MVV, and an extended time of opening windows in winter was significantly associated with a lower prevalence of impaired FEV6. While, opening windows for a longer time in autumn was significantly associated with higher prevalence of impaired FEV6 and FEV1/VC. Home renovations, doing physical exercise for more than 30 min per day, air pollution exposure during commuting, sleeping in own rooms, height stunting, and preterm birth were significantly associated with an increased risk of impaired lung function. Breastfeeding, having a father with a white-collar profession and with a higher education level were positively associated with the lower prevalence of impaired lung function. Impaired lung function is commonly found in school children in Wuhan, nowadays. Breastfeeding, opening windows long-term in summer and winter, higher socioeconomics, and an urban living environment were protective factors for impaired lung function. However, opening windows long-term and using air conditioning short-term in autumn, as well as home renovations, doing physical exercise for more than 30 min per day, preterm birth, height stunting, and air pollution exposure during commuting were regarded as significant risk factors for impaired lung function. Promoting breastfeeding, lengthening window opening times in winter and summer, and controlling household renovation and air pollution exposure during commuting are recommended to reduce the risk of impaired lung function in children in Wuhan.