Objective To investigate the characteristics of the pathogens causing bloodstream infection after general surgery in infant and young children patients, and to provide the references for disease treatment and nosocomial infection control. Methods The clinical and laboratory examination data after general surgery in infant and young children patients, who were admitted to our hospital from January 2012 to March 2017, were retrospectively collected. The pathogens and drug resistance were analyzed by SPSS 18.0 software. Results In this study, 109 cases were included, and 117 strains of the pathogens were isolated, including 53 isolates (45.3%) of gram negative bacteria, 41 isolates (35.0%) of gram positive bacteria, and 23 isolates (19.7%) of fungi. Escherichia coli (16/117, 13.7%), Enterococcus faecium (13/117, 11.1%), Candida parapsilosis (12/117, 10.3%), Klebsiella pneumoniae (9/117, 7.7%) and Enterococcus faecalis (8/117, 6.8%) were the top 5 species. Strains producing extended-spectrum beta-lactamase accounted for 87.5% of E. coli (14/16) and 44.4% (4/9) of K. pneumoniae isolates. Both E. faecium and E. faecalis were susceptible to vancomycin. C. parapsilosis showed the susceptibility to the antifungal agents. Conclusion Gram negative bacteria are predominant pathogens causing bloodstream infection after general surgery in infant and young children patients, and infection caused by resistant isolates should be prevented and controlled.