In order to explore the mechanism of aquaporin (AQP) in response to drought stress in Artemisia ordosica, we amplified the AQP gene by RACE using A. ordosica in the Qaidam Basin of Qinghai Province. The fulllength gene of AQP was obtained and the structure of AQP protein was predicted and analyzed. At the same time, qRTPCR was used to analyze the expression patterns of AQP gene of A. ordosica in different degrees of drought stress and different tissues. The results showed that: (1) the 746 bp fragment 1 and the 534 bp fragment 2 of AQP gene were successfully cloned. The fulllength cDNA sequence was obtained after splicing. The total length of AQP gene of A. ordosica was 864 bp. (2) Subcellular localization indicated that the AQP gene of A. ordosica was located on the cell membrane. The homology alignment showed that the A. ordosica had high similarity with the AQP genes of plants such as Helianthus annuus, Lactuca sativa and Hevea brasiliensis. Structural prediction indicated that the AQP protein contained six transmembrane helix structures and was weak in hydrophilicity. In the protein secondary structure, αhelix and random coil were the main constituent elements. (3) According to qRTPCR analysis, the result showed that AQP gene of A. ordosica showed regular changes with the increase of drought stress. The expression of AQP gene was upregulated in roots, stems and leaves, the highest was in leaves. So the above results indicated that the AQP gene had distinct structural characteristics and expression patterns to adapt to drought stress. This study provided the foundation for further characterizing the mechanism of A. ordosica drought resistance.