The effects of rootstocks tomato (Solanum lycopersicum L.), eggplant (Solanum melongena L.), and nightshade (Solanum nigrum L.) grafting on the growth and selenium (Se) accumulation of Cyphomandra betacea Sendt. seedlings were studied to identify the most suitable rootstock for increasing Se uptake of fruit trees grown in Se-contaminated soil. The rootstocks of tomato, eggplant, and nightshade grafting increased the scion biomass of C. betacea seedlings by 146.1%, 23.2%, and 94.5%, respectively, compared with the un-grafted seedlings. Moreover, tomato, eggplant, and nightshade rootstocks grafting increased the photosynthesis, superoxide dismutase activity, and peroxidase activity, while reducing the catalase activity and soluble protein content of C. betacea seedlings. Although all three rootstocks grafting decreased Se contents in rootstock roots and stems, only nightshade rootstock grafting increased Se content in the scions of C. betacea seedlings. Notably, root biomass, catalase activity, soluble protein content, rootstock root Se content, and rootstock stem Se content were closely related to the scion Se content. These findings suggest that only grafting onto nightshade rootstock significantly enhances Se uptake in C. betacea, whereas tomato and eggplant rootstocks grafting have no effect on Se uptake.