BackgroundCarbapenem-resistant gram-negative bacilli (CR-GNB) have been increasingly reported in China. However, dynamic monitoring data on molecular epidemiology of CR-GNB are limited in pediatric patients.Results300 CR-GNB isolates (200 Carbapenem-resistantK. pneumoniae (CRKP), 50 carbapenem-resistantA.baumannii(CRAB) and 50 carbapenem-resistantP. aeruginosa(CRPA)) were investigated. The predominant carbapenemase gene wasblaNDM−1(73%) andblaKPC−2(65%) in neonates and non-neonates. Meanwhile, the predominant STs were ST11 (54%) in neonates and ST17 (27.0%) and ST278 (20.0%) in non-neonates. Notably, a shift in the dominant sequence type of CRKP infections from ST17 /ST278-NDM-1 to ST11-KPC-2 was observed during the years 2017–2021 and KPC-KP showed relatively higher resistance to aminoglycosides and quinolones than NDM-KP.BlaOXA−23was isolated from all the CRAB isolates while only one isolate expressingblaBICand 2 isolates expressingblaVIM−2were found in CRPA isolates. ST195 (22.0%) and ST244 (24.0%) were the most common in CRAB and CRPA isolates and all the STs of CRAB belonged to CC92 while CRPA presents ST types with diversity distribution.ConclusionCRKP showed different molecular phenotypes in neonates and non-neonates and was changing dynamically and high-risk clone of ST11 KPC-KP should be paid more attention. Most CRKP and CRAB strains shared the same CCs, suggesting that intrahospital transmission may occur, and large-scale screening and more effective measures are urgently needed.