Objective To investigate the relationship between resistance phenotype and distribution of active efflux system (efflux pump) genes as well as New Delhi metallo-β-lactamase (NDM-1) in Acinetobacter baumannii (A.baumannii). Methods The minimal inhibitory concentrations (MICs) of 13 antimicrobial agents against 81 A.baumannii clinical isolates were determined by agar dilution method. The phenotype of efflux pump was determined by the changes of MICs after treatment with efflux pump inhibitor PAβN. The distribution of efflux pump genes adeABC, adeIJK and adeFGH and NDM-1 gene blaNDM-1 in clinical isolates was detected by PCR, the clinical isolates were grouped according to the detection findings of efflux pump genes, and the resistance rates were compared among groups. Results Eighty-one A.baumannii clinical isolates were resistant to 13 common antimicrobial agents. There were active efflux pump in 43(53%) clinical isolated strains. The resistance rate was lowest (30.9%) to minocycline and second lowest to imipenem, and those to all the others were over 60%. The resstance rates to cefoxitin and co-trimoxazole were 97.5％and 93.8％ respectively, which were relatively higher. In clinical isolates with positive AdeABC efflux pump genes, the detection rates of adeB, adeS and adeR were 78%, 78%, 74% respectively. In AdeJ and AdeFGH efflux pump genes, the detection rates of adeJ, adeL, adeF, adeG and adeH were all over 90%. The multi-drug resistance of the 60 isolates with positive efflux pump genes adeB, adeJ and adeG were most serious, and the resistance rates of gene-positive groups were significantly higher than gene-negative groups. In addition, 32 A.baumannii clinical isolates were detected to carry blaNDM-1 gene. Conclusion The multi-drug resistance of A.baumannii clinical isolates in the region is serious, and there exists clonal spread of blaNDM-1 gene. The detection rates of efflux pump genes AdeABC, AdeIJK and AdeFGH in A.baumannii clinical isolates are relatively higher. Active efflux pump system and NDM-1 play an important role in the multi-drug resistance of A.baumannii.