Inborn errors of immunity (IEI) patients with different immune component deficiencies are susceptible to different bacteria. This study aimed to investigate the spectrum of bacterial infection in different classifications of IEI in children. Pediatric patients diagnosed with IEI and detected positive for bacteria considered to be pathogenic were included in this retrospective study. In this study, 1818 medical charts of IEI inpatients were reviewed, and 291 hospitalizations were enrolled, including 244 IEI patients. A total of 363 strains were detected, of which, 84 (23.14%) were gram-positive bacteria, and 279 (76.86%) were gram-negative bacteria. The main bacteria isolated from different IEI classifications were different. Klebsiella pneumoniae (12.68%) and Pseudomonas aeruginosa (12.68%) were most isolated from combined immunodeficiencies. Haemophilus influenzae (31.86%) and Moraxella catarrhalis (14.16%) were most isolated from predominant antibody deficiencies. K. pneumoniae (15.68%) and Escherichia coli (11.89%) were most isolated from congenital defects of phagocytes. Specific bacteria had susceptible classifications of IEI. H. influenzae was often isolated in predominant antibody deficiencies (7.83%), Salmonella was often isolated in defects in intrinsic and innate immunity (4.28%), and Staphylococcus aureus was often isolated in combined immunodeficiencies with syndromic features (5.77%). The ratios of methicillin-resistant S. aureus, carbapenem-resistant E. coli, K. pneumoniae, P. aeruginosa, and Acinetobacter baumannii in IEI patients were 55.17%, 38.10%, 25.71%, 25.81%, and 70.59%, respectively, which were higher than those in non-IEI patients. The IEI in children defines a unique and specific spectrum of bacterial infections. Isolated bacteria from children with IEI have high antimicrobial resistance.