Objective To analyze and discuss the epidemiological characteristics and drug resistance of pathogenic bacteria of infective endocarditis in Nanjing in the past five years, and to provide reference for the prevention and treatment of infective endocarditis. Methods A total of 220 infective endocarditis cases in Nanjing area from 2015 to 2020 were included in the analysis. The distribution characteristics of pathogens were collected and analyzed. Information on drug resistance was also collected, and the potential relationship between pathogen distribution and drug resistance was explored. Statistical analysis was performed using SPSS 19.0. Results The ratio of male to female patients included in this study was 143:77, and most of them were aged from 41 to 60 years old. There were 195 patients with underlying cardiac diseases (88.64%). A total of 1132 pathogenic bacteria were detected in the blood samples of all 220 patients, among which 1 007 were mainly gram-positive bacteria (88.96%): 725 strains of Streptococcus viridans (725/1 132, 64.05%), 124 strains of Staphylococcus aureus (124/1 132, 10.95%), 96 strains of Staphylococcus epidermidis (96/1 132, 8.48%), and 62 strains (62/1 132, 5.48%) of others (Staphylococcus human, etc.); the main gram-negative bacteria ( a total of 125 strains , 11.04%) were 73 strains of Pseudomonas aeruginosa (73/1 132, 6.45%) and 52 strains of Escherichia coli (52/1 132, 4.59%). Among the strains isolated from subjects of different ages and genders, the distribution difference was consistent with the total trend, and there was no significant difference (all P>0.05). Among gram-positive bacteria, Streptococcus was sensitive to antibiotics such as penicillin, oxacillin, and vancomycin. Staphylococcus aureus and S. epidermidis were sensitive to vancomycin and resistant to oxacillin and penicillin. Gram-negative bacteria were less resistant to amikacin and meropenem. All these differences were statistically significant (all P<0.05). Conclusion For patients with infective endocarditis, antibiotics should be selected reasonably according to the type of pathogenic bacteria and the corresponding drug resistance characteristics.