A study in the Neonatal Department of Maternity Hospital in HCM, Vietnam, in 2019 reported that the prevalence of Carbapenemase-producing Enterobacteriaceae (CPE) was 42.20% (n = 83). However, risk factors of CPE colonization and transmission were still an unsolved question. Hence, we implemented this study. A prospective study was conducted from April to July 2020 at the Childbirth Ward of Hung Vuong Hospital, where 359 pairs of mothers and their neonates participated in our research. We applied laboratory methods to confirm CPE colonization and its antibiotic resistance, including rectal swab tests, chromo-carba plates, MALDI-TOF method, antibiograms, and rep-PCR method. The 23.0 version of SPSS was a software to analyze personal characteristics, prevalence, and risk factors for CPE colonization. Adjusted odds ratio and 95% confidence interval were considered significant at P < 0.05. The results showed that the prevalence of CP E. coli transmission between mothers and neonates was 0.28% (1/359), confirmed by the rep-PCR method. The characteristics that reduced the CPE-colonization risks in mothers were the mother’s age (19-23 years old), vaginal delivery, mothers caring for neonates, skin-to-skin contact time, and breastfeeding. However, the risk factors that increased the CPE colonization in neonates were the NICU admission before fecal sampling and the number of vaginal examinations performed on mothers before delivery. Although the prevalence of mother-to-neonate CPE transmission was low, screening for CPE colonization at hospital admission, adhering to hand hygiene, and implementing aseptic medical practices are crucial standards for preventing and controlling CPE colonization in the healthcare sector.