It has been defined that deficiency of trace elements plays an important role in the progression of asthma. However, the relationship between blood zinc (Zn), selenium (Se), and magnesium (Mg) and pulmonary functions in children remains to be clarified. A cross-sectional study was conducted in Wuxi, China, and a total of 202 healthy children were recruited. The forced vital capacity volume (FVC) and forced expiratory volume in the 1┬ás (FEV1) were measured. Blood samples were collected, and the levels of blood zinc, selenium, and magnesium were measured by inductively coupled plasma mass spectrometry (ICP-MS). Meanwhile, the concentrations of serum total IgE was also determined. The associations between trace elements and pulmonary functions were analyzed by multiple linear regression models. After stratified by sex, there was a positive association between blood Zn and pulmonary functions in boys. In addition, blood Zn was also negatively associated with serum total IgE concentrations in boys, but not in girls after adjusting for potential confounders. Our findings indicated that zinc deficiency was significantly related to children’s pulmonary functions and that screening of trace elements may be a potential solution to decrease the risks of asthma in children.