Abstract Background This study aims to compare pathogens and their antibiotic resistances of burn patients from burn intensive care unit (ICU) or common burn ward. Of 2395 clinical samples from 63 patients in burn ICU, pathogens were detected in 1621 samples, in which 1203 strains (74.2%) were Gram negative bacteria, 248 strains (15.3%) were Gram positive bacteria, 170 strains (10.5%) were fungi. Top-4 microorganisms isolated from patients in burn ICU were Bauman's Acinetobacter (557, 34.4%), Pseudomonas aeruginosa (287.17.7%), Staphylococcus aureus (199, 12.3%) and Klebsiella pneumoniae (171, 10.5%). Of 512 clinical samples from 235 patients in common burn units, pathogens were detected in 373 samples, in which 189 (50.6%) strains were Gram negative bacteria, 150 strains (40.2%) were Gram positive bacteria, 34 strains (9.2%) were fungi. Top-4 microorganisms isolated from patients in common burn units were S. aureus (103, 27.6%), P. aeruginosa (46, 12.3%), K. pneumoniae (38, 10.2%) and Escherichia coli (32, 8.6%). Antibiotic resistance rates of pathogens isolated from clinical samples of burn patients from ICU was significantly higher than those from common units. Conclusions Pathogens and their antibiotic resistances are significantly different between burn ICU and common burn units. This finding has great implication for infection control in burn patients.