Objective To analyze the rates of drug resistance of carbapenem-resistant Klebsiella pneumoniae (CRKP) and extended-spectrum β-lactamase-producing Escherichia coli (ESBL-E.coli) in bronchoalveolar lavage fluid (BALF) of critically ill patients with severe pneumonia and artificial airway and risk factors of CRKP. Methods Patients with severe pneumonia and artificial airway treated in the Center of Emergency and Intensive Care Unit, Jinshan Hospital, Fudan University from May 2022 to May 2025 were selected. Klebsiella pneumoniae (K. pneumoniae) and Escherichia coli (E.coli) isolated and cultured from BALF of these patients were analyzed. The drug resistance rates of the two bacteria were compared. The multivariate logistic regression was used to analyze related risk factors for CRKP infection. Results A total of 384 patients were included, and 384 strains were cultured, including 330 strains (85.9%) of K. pneumoniae and 54 strains (14.1%) of E.coli. The infection rate of K. pneumoniae was higher. Compared with E.coli, the drug-resistant gene expression rate of K. pneumoniae was lower (37.3% vs 57.4%, P＜0.01). The resistance rates of CRKP to cefotaxime, cefepime, aztreonam, and imipenem were higher than those of ESBL-E.coli (P＜0.003). Both CRKP and ESBL-E.coli had high sensitivity to polymyxin and tigecycline. Multivariate logistic regression showed duration of mechanical ventilation ≥ 7 days, and combination of ≥ 2 antibiotics for over 7 days were independent risk factors for CRKP infection (P＜0.01). Conclusions For patients with severe pneumonia and artificial airway in ICU, K. pneumoniae is the main bacterial infection. CRKP and ESBL-E.coli in BALF exhibit different degrees of drug resistance to various antibacterial agents, both have the characteristic of multidrug resistance, and are sensitive to polymyxin and tigecycline. Prevention and control of risk factors related to CRKP should be formulated particularly.