The relationship between cesarean section (CS) and allergic disorders such as asthma and wheezing has been inconsistent, and the mechanisms for their connection remained largely unknown. We aimed to investigate whether CS is associated with infantile wheeze and to explore the connection between CS and several risk factors known to correlate with allergy development. Mononuclear cells were isolated from cord blood and assessed for cytokine responses by ELISA. Bacteria from nasopharyngeal specimens were identified with traditional culture methods. Infant lung function tests were performed at 6 and 12 months of age. IgE levels and clinical outcomes were assessed at 12 months. The result showed that children delivered by CS were associated with increased risk of wheezing (aHR 1.63; 95% CI: 1.01-2.62) and decreased compliance of the respiratory system at 12 months (p = 0.045). In addition, CS was associated with reduced TLR1-2- triggered TNF-α and IL-6 responses at birth. By12 months of age, children delivered by CS had significantly less airway bacterial clearance. Our findings suggested that CS was associated with decreased pro-inflammatory cytokine response to TLR1-2 stimulation, followed by higher abundance of bacterial colonization in the airway during late infancy, thus increasing the risk of infantile wheezing.