Objective　To analyze the risk factors of multiple bacterial infection in neonates with severe pneumonia in neonatal intensive care unit (NICU). Methods　The clinical data of 1057 newborns with severe bacterial pneumonia admitted to the NICU from January 2014 to May 2019 were retrospectively analyzed, and the risk factors for multiple bacterial infections were analyzed. Results　Univariate analysis showed that 12 factors including gestational age (<37 weeks), birth weight (<2500 g), onset age (<7 days), infection type (nosocomial infection), hospital stays (≥14 days), mechanical ventilation, Apagar score (<7 points), premature rupture of membranes, days of antibiotics use (≥10 days), changes of antibiotics (≥3) and combined use of antibiotics (≥3) were risk factors for the multiple bacterial infections in neonates with severe pneumonia in NICU, and differences were statistically significant (P<0.05). Multivariate analysis showed that changes of antibiotics (≥3), Apagar score (< 7 points), type of infection (nosocomial infection), mechanical ventilation and amniotic fluid contamination (degree II and III) were independent risk factors for the multiple bacterial infections in neonates with severe pneumonia in NICU (P<0.05). Conclusions　Comprehensive prevention and control measures should be taken in the clinic for the main risk factors to reduce multiple bacterial infections of neonates with severe pneumonia in NICU.