Objective To explore the distribution and difference in antimicrobial resistance of pathogens in diabetic patients complicated with pulmonary infection during different disease courses, so as to provide reference for rational choice of antimicrobial agents in clinic. Methods Patients with type 2 diabetes mellitus complicated with pulmonary infection in a hospital between January 2015 and October 2018 were selected, they were divided into long-term disease course group (LC group, disease course ≥ 10 years) and short-term disease course group (SC group, disease course<10 years), qualified sputum specimens were collected for bacterial culture and antimicrobial susceptibility testing, and the monitoring data were analyzed statistically. Results A total of 132 cases in LC group and 127 in SC group were included. 385 strains of pathogens were isolated, 201 of which were isolated from LC group and 184 were from SC group. Proportion of gram-negative bacteria and fungi isolated from LC group was higher than that of SC group, and gram-positive bacteria was lower than that SC group; proportion of Acinetobacter baumannii from LC group was higher than that of SC group, Staphylococcus aureus in LC group was lower than that of SC group; differences were all statistically significant (all P<0.05). Isolation rates of extended-spectrum beta-lactamases (ESBLs) and methicillin-resistant (MR) strains in LC group were both higher than those in SC group (40.87% vs 22.03%; 37.50% vs 19.61%, respectively), with statistical significance (both P<0.05). Antimicrobial susceptibility testing results showed that resistance rates of Klebsiella pneumoniae and Escherichia coli to cefuroxime and levofloxacin were both>50%; resistance rates of Acinetobacter baumannii to ampicillin/sulbactam, piperacillin/tazobactam, ceftazidime, levofloxacin and tobramycin were all ≥ 50%;resistance rates of Pseudomonas aeruginosa to levofloxacin, ciprofloxacin and tobramycin were all >50%; resistance rate of Staphylococcus aureus to cefazolin, ceftriaxone, clindamycin, azithromycin and gentamicin were all ≥ 50%. Resistance rates of Pseudomonas aeruginosa to piperacillin/tazobactam, ceftazidime, imipenem and amikacin in LC group were all higher than those in SC group (all P<0.05). Conclusion Distribution of pathogens and antimicrobial resistance of partial bacteria in diabetic patients complicated with pulmonary infection during different disease courses are different, which should be treated differently in clinic.