Grafting is an important process to propagate horticulture plants; however, the mechanism through which the scion affects the absorption of rootstock remains poorly understood. The effects of the scion on AM fungi types in the rhizosphere soil of rootstock and the absorption of mycorrhizal root were determined in this study. Composition of arbuscular mycorrhizal (AM) fungi, soil assessment, spore density, hyphal length density, glomalin-related soil protein (GRSP) content in rhizosphere soil, root hair morphology and AM colonisation rate were measured among Kampong' avocado rootstocks grafted with five scions and Kampong' seedling trees. Results showed the main types of AM fungi in avocado seedling trees and trees grafted with five scions were nearly identical. However, the proportion of main genera exhibited differences. In addition, alkali-hydrolysable N, alkali-hydrolysable P and available K in rhizosphere soil, root hair density, AM colonization, spore density, hyphal length and GRSP content suggested the absorption of Kampong' rootstocks grafted with Monroe', Wilson seedless', Hass' and Tonnage' possessed stronger absorption than Kampong' seedling trees because of high AM colonisation and root hair density. This study suggested scions regulated both the AM and root hair development systematically and laid the foundation for future research of AM-enhancing avocado production.