Water stress is one of the most critical abiotic stresses that restricts growth, development, and alters physiological and biochemical mechanisms of plant. The effects of long‐term water shortage‐induced oxidative stress on morphophysiological parameters, proline metabolic genes, and artemisinin content were studied in Artemisia annua L. under greenhouse conditions. Plant growth, biomass accumulation, relative water content, and chlorophyll content were reduced under drought. Leaf water potential ranged from −0.3248 MPa to −1.22 MPa in stress conditions. Increased levels of proline accumulation, protein concentration, and lipid peroxidation were detected in water‐stressed plants. Stage‐dependent increases in activity of antioxidants including superoxide dismutase, ascorbate peroxidase, glutathione reductase, monodehydroascorbate reductase, and dehydroascorbate reductase were observed. The expression of proline biosynthetic genes including pyrroline‐5‐carboxylase synthase1, 1‐pyrroline‐5‐carboxylase synthase2, and 1‐pyrroline‐5‐carboxylase reductase was induced, while the ornithine aminotransferase transcript showed a variable response and the expression of proline catabolic genes including proline dehydrogenase1, proline dehydrogenase1, and proline 5‐carboxylate dehydrogenase was reduced by water stress. Our results indicate that the glutamine pathway is predominant under drought stress in A. annua and a reduction of catabolic gene expression is adopted as a defense strategy in adverse conditions. Higher expression of biosynthetic genes and lower expression of catabolic genes at the preflowering stage confirmed the important role of proline in flower development. Artemisinin content decreased owing to water stress, but the slightly higher amounts were detected in leaves of severely stressed plants compared with moderately stressed plants. The artemisinin content of A. annua might be regulated by controlling irrigation regimes.