2124 neonates were monitored from February 2013 to August 2014, among which 1119 were admitted from outpatient department (outpatient group), 782 were transferred from other departments (other department group), and 223 were from other hospitals (other hospital group). Through it we explore the distribution of multidrug resistant organism in neonates, which were admitted to the hospital through various ways, and therefore analyze the risk factors of nosocomial infection to avoid cross infection of multi drug resistant organism in neonatology department. The results showed that 105 strains of multi drug resistant bacteria were detected in the neonatal department. Among them, there were 57 strains from the outpatient group, 27 from the other department group, and 21 from the other hospital group. Neonates with the hospitalization time of more than 14 days and low birth weight infants (1500 g) were the high-risk groups of drug-resistant strains in nosocomial infection. So the infection in neonates from other departments or hospitals should be strengthen, especially the prevention and control in neonates with the hospitalization time than 14 days and low birth weight infants (1500 g) in order to reduce the occurrence of multiple drug-resistant strains cross infection.