Klebsiella pneumoniae carbapenemase genes (bla_KPC) play an important role in carbapenem-resistant Enterobacteriaceae in China. A rapid detection method for bla_KPC genes and investigations into the molecular characteristics of bla_KPC positive Klebsiella pneumoniae were necessary. In this study, an easy and rapid recombinase aided amplification assay (RAA) for bla_KPC was established. This protocol could be completed at 39°C in 15–20 min. The sensitivity of this assay was determined as 48 copies per reaction, and the specificity was 100%. The bla_KPC RAA method could be used for clinical diagnosis and epidemiological investigation. Among 801 fecal samples from inpatients, 34 bla_KPC positive isolates were identified from each sample, of which 23 isolates were K. pneumoniae. ST11 with bla_KPC-2 was the most prevalent type. All these strains were multidrug resistant and carried various virulence genes. Fecal carriage of bla_KPC positive carbapenem-resistant K.pneumoniae poses significant challenges for public health control.