The invention discloses a molecular recognition method for rootstock-scion combination and selection in efficient old tea-oil tree and camellia grafting. According to the method, old tea-oil trees serve as rootstocks, camellia serves as scions, and the molecular recognition method of efficient grafting rootstock-scion combination and selection is obtained in the following steps that 1, the DNA of the old tea-oil trees and the DNA of the camellia are extracted; 2, a proper SSR labeling primer is screened; 3, the Dice heredity coefficients between different varieties of old tea-oil trees and different varieties of camellia are detected; 4, a rootstock-scion combination is designed according to the Dice heredity coefficients; 5, according to the rootstock-scion combination, the camellia is grafted through the old tea-oil trees. The rootstock-scion combination, with the Dice heredity coefficient range being 0.551-0.600 and 0.751-0.800, obtained through the molecular recognition method is good in grafting compatibility, high grafting disease morbidity is low, the grafting survival rate is as high as over 84%, the high grafting disease morbidity is lower than 4%, and the rootstock-scion combination can be conveniently applied and popularized in market.