This study investigated the effects of fermentation with kefir grains on the nutritional composition, flavor, and physical stability of hemp seed, and explored its potential as a probiotic plant-based beverage. After fermentation of a homogenized hemp seed water suspension, the concentrations of organic acids (lactic, acetic, tartaric, butyric, succinic, and malic acids) increased. The content of nutritional components, amino acids, and free fatty acids increased, as well as the number (from 16 to 21) and concentrations of flavor compounds, such as alcohols, acids, and esters. Fermentation also increased the particle size, viscosity, and phase-separation resistance of the final product. Therefore, kefir grains improved the nutritional composition, flavor, and physical stability of the hemp seed beverage, indicating its potential as a functional beverage, and providing a theoretical basis for the development of plant-based fermented beverages.