The rot and deterioration of sprouts are closely related to their physiological state and postharvest storage quality. The study investigated the influences of brassinolide, zeaxanthin, and their combination on physiological metabolism, chlorophyll fluorescence, and nutritional quality of radish sprouts stored at 4 °C. The combined treatments enhanced hypocotyl length, fresh weight, contents of secondary metabolites, nutritional ingredients, glutathione, the photoprotective capacity of PSII, and FRAP level in radish sprouts compared with zeaxanthin alone. The combined treatments enhanced hypocotyl length, fresh weight, glutathione content, Fv/Fm value, and antioxidant capacity in sprouts compared to brassinolide alone. The combined treatment of zeaxanthin and brassinolide could make radish sprouts keep high biomass and antioxidant capacity by increasing the contents of stress-resistant metabolites and by weakening the photoinhibition of PSII in radish sprouts stored at 4 °C.