Objective To understand the molecular epidemiological characteristics and hypervirulence evolution trend of ST11 carbapenem-resistant Klebsiella pneumoniae (CRKP) isolated from medical institutions in Shanghai, and provide scientific basis for formulating the prevention and control measures of drug-resistant organisms. Methods A total of 201 strains of CRKP isolated from 12 medical institutions in Shanghai from 2021 to 2022 were collected. Antimicrobial susceptibility testing and whole genome sequencing were performed. The concatenated data was used for multilocus sequencing typing (MLST), serum typing (wzi typing), as well as analysis of resistance and virulence genes. Results All 201 CRKP strains were multidrug-resistant organisms (MDROs). These strains were almost completely resistant to carbapenems, cephalosporins, and quinolones. Drug resistance gene analysis showed that 93.03% of CRKP strains carried KPC gene. 201 CRKP strains were divided into 6 ST types and 10 capsule wzi types, with ST11-KL64 (n=104) being the dominant type, followed by ST15-KL19 (n=54). 52.24% (n=105) of CRKP carried rpmA/rpmA2+iucA+iutA+iroN genes. Conclusion CRKP isolated from medical institutions in Shanghai is mainly ST11-KL64 type with severe multidrug resistance, and more than half of the strains are hypervirulent carbapenem-resistant Klebsiella pneumoniae (hv-CRKP). It is necessary to continuously strengthen the monitoring of the molecular characteristics of CRKP, so as to prevent outbreaks of healthcare-associated infection.