Objective To investigate the distribution and drug resistance of pathogens isolated from respiratory secretion of hematological patients with agranulocytosis accompanied by pulmonary infection in Shanghai. Methods Clinical data and drug susceptibility result of bacteria isolated from respiratory secretion of hospitalized patients with agranulocytosis and pulmonary infection in departments of hematology in 12 hospitals of Shanghai between January 2012 and December 2014 were retrospectively collected, distribution of pathogenic bacteria and drug susceptibility data were analyzed, difference among pathogenic bacteria in different primary diseases was compared. Results A total of 623 strains of pathogenic bacteria were isolated, 138 (22.2%) of which were gram-positive bacteria, 485 (77.8%) were gram-negative bacteria, 60.2% of (292 strains) gram-negative bacteria were non-fermentative bacteria. Constituent ratio of gram-positive bacteria isolated from patients with lymphoma (35.0%) was higher than patients with acute myeloid leukemia and acute lymphoblastic leukemia. The top five bacteria were Stenotrophomonas maltophilia (104 strains, 16.7%), Klebsiella pneumoniae (88 strains, 14.1%), Acinetobacter baumannii (62 strains, 10.0%), Pseudomonas aeruginosa (56 strains, 9.0%) and Staphylococcus aureus (48 strains, 7.7%). Susceptibility rate of Klebsiella pneumoniae to carbapenems was>98%, resistance rates of Pseudomonas aeruginosa to imipenem and meropenem were 24.3% and 8.9% respectively, susceptibility rate of Stenotrophomonas maltophilia to levofloxacin, minocycline and compound sulfamethoxazole was more than 90%, resistance rate of Acinetobacter baumannii to amikacin, cefoperazone/sulbactam was less than 10%. Isolation rate of methicillin-resistant Staphylococcus aureus was 71.4%, no vancomycin-resistant, teicoplanin-resistant and linezolid-resistant Staphylococcus aureus were found. Conclusion Gram-negative bacteria accounts for the majority of isolates from respiratory secretion of patients with agranulocytosis and pulmonary infection, non-fermentative bacteria accounted for more than 50%, the overall bacterial resistance rate is lower than that of CHINET nationwide large sample surveillance.