Aims <p>Soil salinization is a major global problem and an important environmental factor threatening crop production. Yam (<i>Dioscorea opposita</i> Thunb.) is the fourth important root and tuber crop and is known for its substantial vegetable and medicinal properties. Anthocyanins serving a pivotal function in plant resistance to saline-alkali stress, but the regulatory mechanism of yam anthocyanins under saline-alkali stress is not fully understood. Here, the mechanism underlying salt-alkali resistance in high-anthocyanin purple yam was investigated.</p> Methods <p>The root morphological, anthocyanin content, leaf anatomical structure, malondialdehyde content, antioxidant enzyme activity and the RNA-seq were investigated after yam seedlings exposure to saline-alkali stress treatments.</p> Results <p>Saline-alkali stress could markedly inhibit the growth of yam bulbil seedlings and induce the production of purple plants. The thickness of the upper epidermis and spongy tissue, and the malondialdehyde content of the purple leaces were significantly lower than those of the green ones, while the thickness of lower epidermis was significantly increased. Meanwhile, compared with the purple seedlings, the enzymatic activities of superoxide dismutase, peroxidase and catalase in the the green plants were significantly increased. Furthermore, RNA-seq of purple and green yam seedlings subjected to saline-alkali stress identified substantial differences in differentially expressed genes, which were predominantly enriched in metabolic pathways or factors influencing anthocyanin synthesis.</p> Conclusions <p>Saline-alkali stress resulted in an increase in anthocyanin content and modifications in leaf morphology, thereby enhancing the stress resistance of yam. These data provided a basis for further exploration of the role of anthocyanins in saline-alkali stress in tuber crops.</p>