Selenium (Se), as a vital stress ameliorant, possesses a beneficial effect on mediating detrimental effects of environmental threats. However, the mechanisms of Se in mitigating the deleterious effects of drought are still poorly understood. Gentiana macrophylla Pall. is a well-known Chinese medicinal herb, and its root, as the main medicinal site, has significant therapeutic effects. The purpose of this experiment was to investigate the functions of Se on the seedling growth and physiobiochemical characteristics in G. macrophylla subjected to drought stress. The changes in microstructure and chloroplast ultrastructure of G. macrophylla leaves under drought exposure were characterized by scanning electron microscopy (SEM), scanning electron microscopes and energy dispersive X-Ray spectroscope (SEM-EDX), and transmission electron microscopy (TEM), respectively. Results revealed that drought stress induced a notable increase in oxidative toxicity in G. macrophylla, as evidenced by elevated levels of hydrogen peroxide (H2O2), lipid peroxidation (MDA), enhanced antioxidative response, decreased plant photosynthetic function, and inhibited plant growth. Chloroplasts integrity with damaged membranes and excess osmiophilic granule were observed in the drought-stressed plants. Se supplementation notably recovered the stomatal morphology, anatomical structure damage, and chloroplast ultrastructure of G. macrophylla leaves caused by drought exposure. Exogenous Se application markedly enhanced SPAD, photosynthetic stomatal exchange parameters, and photosystem II activity. Se supplementation significantly promoted the activities of superoxide dismutase (SOD), ascorbate peroxidase (APX), and catalase (CAT), while reducing levels of MDA, superoxide anion (O2–.) and H2O2, and improving membrane integrity. Furthermore, the ameliorative effects of Se were also suggested by increased contents of osmotic substances (soluble sugar and proline), boosted content of gentiopicroside and loganinic acid in roots, and alleviated the inhibition in plant growth and biomass. Fourier transform infrared (FTIR) analysis of Se-treated G. macrophylla roots under drought stress demonstrated that Se-stimulated metabolites including O-H, C-H, N-H, C-N, and CO functional groups, were involved in resisting drought stress. Correlation analysis indicated an obvious negative correlation between growth parameters and MDA, O2–. and H2O2 content, while a positive correlation with photosynthetic gas exchange parameters. Principal component analysis (PCA) results explained the total variance into two principal components contributing the maximum (93.50 %) among the drought exposure with or without Se due to the various experiment indexes. In conclusion, Se exerts beneficial properties on drought-induced detrimental effects in G. macrophylla by relieving oxidative stress, improving photosynthesis indexes, PSII activity, regulating anatomical changes, altering levels of gentiopicroside and loganinic acid, and promoting growth of drought-stressed G. macrophylla.