Purpose: To solve the reproduction problem of Catalpa bungei and promote the development and utilization of its resources, we selected different C. bungei graft combinations and compared the effects of different rootstock cultivars on the growth and development of C. bungei.Methods: Ten C. bungei grafting combinations consisting of two rootstocks and five scions were included in this study. Differences in plant growth, root development, physicochemical properties, soil environment, bacterial community composition, and diversity were compared for different scion/rootstock combinations.Results: The results showed that the early grafted seedlings of C. ovata dominated plant growth and root development, but there was obvious incompatibility between the rootstock and scion. The high affinity of C. fargesii f. duclouxii rootstock is beneficial for the sustained and healthy development of grafted seedlings. Moreover, rootstock cultivars caused differences in the rhizosphere bacterial composition and diversity of different C. bungei scion/rootstock combinations. The composition of the C. fargesii f. duclouxii rootstock bacterial community was more diverse, whereas the C. ovata rootstock had more specific bacterial taxa. Pearson analysis showed that a large number of growth indicators of grafted seedlings were significantly correlated with dominant bacteria in the root soil.Conclusion: C. fargesii f. duclouxii is a suitable choice for grafting C. bungei to the south of the Yangtze River in China. Rootstock varieties can regulate community ecological functions by influencing the composition and diversity of rhizosphere soil microbial communities, thus affecting scion traits and the growth and development of grafted seedlings.