Kadsura coccinea (Lem.) A. C. Smith and Schisandra sphenantha rehd. et wils. are different genus plants of Schisandraceae, distributed in the north and south of China, respectively. These species are non-wood forest trees with important medicinal value. Grafting is one of the technical means by which plants migrate to other regions to adapt to different habitats. However, the current research on the grafting of Schisandraceae only focuses on the effect of the rootstock on the scion, and lacks investigations on the effect of the scion on the rootstock, leading to the mechanism of the rootstock–scion interaction being still unclear. In this study, Kadsura coccinea (K) and Schisandra sphenanthera (S) were used as scion and rootstock for reciprocal grafting, and four grafted combinations, K/S (scion/rootstock), S/S, S/K, and K/K, were obtained, with S/S and K/K being the controls. Comparative analyses of the morphological, anatomical, and physiological characteristics of rootstocks were conducted at 10 d, 30 d, 50 d, and 70 d after grafting. The results showed that compared with the control, the total root length, root volume, root tips, and root biomass of K/S and S/K decreased. However, the root average diameter and root surface area of K/S increased, while those of S/K decreased. All the differences between the above indices and the control were about 10%, and almost all of them changed most significantly at 70 d after grafting. Anatomically, the root cross section, stele diameter, and xylem area of K/S increased, while those of S/K decreased. In addition, the cortex thicknesses of K/S and S/K increased. These anatomical changes were mainly reflected in the second-order and third-order roots. Meanwhile, the changes in root endogenous hormone (IAA, ZR, GA3, ABA) contents in K/S and S/K in relation to days after grafting could explain the differences in root morphology. Moreover, both K/S and S/K had lower root activity and soluble sugar content than the control, and S/K had lower soluble protein and higher malondialdehyde content. This study indicated that the intergeneric grafting of Schisandraceae inhibited the growth of rootstocks, and the degree of inhibition was potentially related to the relative strength of the rootstock and scion, which provides a theoretical basis for further research on the rootstock–scion interaction mechanism.