Objective To detect the epidemiological characteristics and resistance of carbapenem-resistant Klebsiella pneumoniae (CRKP) in three general hospitals in southwest China, provide basis for the prevention and control of CRKP infection. Methods 159 strains of CRKP isolated in three tertiary first class hospitals in southwest China from January to December 2019 were collected, antimicrobial susceptibility of CRKP strains was detected by micro-broth dilution method, identification and multilocus sequence typing of carbapenemase gene were carried out by polymerase chain reaction (PCR). Clinical information of patients such as invasive procedure, antimicrobial use, laboratory examination and prognosis were compared. Results 50.9% of 159 CRKP strains were from sputum specimens. 94.3% of patients with CRKP infection had received invasive procedure, mortality of patients with bloodstream infection was 66.7%. None of strains were susceptible to carbapenems, resistance rates to levofloxacin and amikacin were 85.5% and 81.1% respectively. Carbapenemase gene was detected in all CRKP strains, detection rate of KPC-2 was 86.8%. ST11 was the most prevalent clone in southwest China. Conclusion The prevalent CRKP strains in southwest China is characterized by high drug resistance, prognosis and outcome of patients with bloodstream infection is poor, it is urgent to strengthen infection control measures and improve prevention awareness.