Objective To explore the drug resistance characteristics of Enterobacter xiangfangensis (E. xiangfangensis) infection in neonatal intensive care unit. Methods Six strains of E. xiangfangensis were isolated from newborns in neonatal intensive care unit from December 2019 to February 2020. These strains were tested for drug resistance using both broth dilution method and disc diffusion method, and 150bp multiple insert size paired-end sequencing was performed using the Illuminanovaseq 6000 to detect drug resistant genes. Meanwhile, clinical data of the children infected with the drug-resistant strains were collected. Results Six strains of E. xiangfangensis were derived from 5 premature infants. One of them was positive in sputum culture, which was considered as colonization. The other 4 infants were sepsis, and 4 cases of sepsis had high risk factors for infection. A premature infant experienced E. xiangfangensis septicemia twice during hospitalization. Drug susceptibility test showed that 6 strains of E. xiangfangensis were sensitive to tigacycline, amikacin and cotrimoxazole. Sensitivity to ciprofloxacin was observed in 1 strain, sensitivity to piperacillin tazobactam was observed in 5 strains, sensitivity to cefoperazone sodium sulbactam was observed in 4 strains, and sensitivity to minocycline was observed in 2 strains. All strains were resistant or intermediate to carbapenems such as meropenem. Identification of the drug resistant genes showed that β-lactam resistance genes blaIMP-4 or laACT-55 and quinolone resistance gene qnrS1 were identified in all 6 strains, aminoglycoside resistance gene aac(6')-Ib4 was found in 5 strains, quinolone resistance gene qnrS1 and sulfonamide resistance gene sul1 coexisted in 5 strains, quinolone resistance genes oqxA9 or oqxB9 also coexisted in 5 strains. Multilocus sequence typing showed that all the 6 strains of E. xiangfangensis had the same sequence type of 148. Conclusions E. xiangfangensis resistance to carbapenems may not be caused by the expression of carbapenem-resistant genes. Antibiotics should be selected reasonably according to the characteristics of bacterial resistance to reduce the generations of resistant bacteria, rather than blindly selecting the carbapenem antibiotics.