The xenia effect refers to the phenomenon whereby the pollen genotype directly affects seed and fruit development during the period from fertilization to seed germination, which leads to different characteristics in phenotypic traits. The xenia effect can create differences in the endosperm and embryo formed after double fertilization and can also alter various fruit parameters, such as the fruit-ripening period; the fruit shape, size, and color; the flavor quality, such as sugars and acids; as well as the nutrient quality, such as anthocyanins. The xenia effect manifests in various ways, playing an important role in increasing the yield of fruit trees, improving fruit appearance and internal quality, as well as in directional breeding. Compared with other pomology research areas, our understanding of the xenia effect is still in its infancy. Currently, xenia is classified into two types: xenia and metaxenia. In the former, the direct effects of the pollen genotype are exhibited in the syngamous parts of the ovules; that is, the embryo and endosperm only. In the latter, the effects of the pollen genotype are demonstrated in structures other than the embryo and endosperm; that is, in tissues derived wholly from the mother plant material, in seed parts such as the nucellus and testa, as well as in the carpels and accessory tissues. However, the current classification has various shortcomings. In the present study, we propose a novel classification based on whether the appearance of xenia results from the tissue formed by double fertilization. Three xenia types are proposed: double-fertilization xenia, non–double-fertilization xenia, and combined xenia. The new classification has great theoretical and practical significance for future studies on the xenia effect and its mechanisms and also provides a more effective, broader application of xenia in improving the yield and quality of fruit trees.