Protracted bacterial bronchitis (PBB) is the common cause of chronic cough in children worldwide, but its etiology has not been fully recognized in China. We retrospectively investigated a total of 66 hospitalized infants under the age of three years with chronic wet cough enrolled in the Affiliated Children's Hospital of Soochow University from October 2010 to March 2014. All patients underwent bronchoscopy and broncho-alveolar lavage (BAL) samples were processed for microbiological and cytological analysis. Of 66 patients with wet cough, 50 (75.8%) were diagnosed with PBB. In the PBB group, wet cough was accompanied by wheezing (90%). Airway malacia were identified in 22 cases (44%). The clinical manifestations of PBB with airway malacia did not differ from those without malacia. Haemophilus influenzae (47.4%) and Streptococcus pneumoniae (36.8%) were the most commonly identified pathogens. Furthermore, CD3(+) and CD3(+)CD4(+) cells were significantly lower in the PBB group (p < 0.01), while CD19(+), CD16(+)CD56(+) and CD23(+) cells were elevated (p < 0.01) in the PBB group. Our study revealed PBB is an important cause of chronic wet cough in Chinese infants, and that changes of lymphocyte subsets are observed in children with PBB. Airway malacia frequently co-existed with PBB, but did not exacerbate the disease.