The phyllosphere microbiome is critical for plant growth and development, but the mechanism by which plants interact with their colonizing microbiome remains elusive. At present, most studies on the interaction between plants and microorganisms focus on the rhizosphere microbiome rather than those of phyllosphere. Moreover, these studies failed to disentangle the mechanism of plant-microbe interactions from the perspective of microbial interaction. In this study, based on the network mapping theory, we correlated the Arabidopsis thaliana genome SNP(Single Nucleotide Polymorphisms) molecular marker data with the microbiome network indices, mined the pivot genes that affected the phyllosphere microbiome network structure to explore the genetic mechanisms how A.thaliana shaped the network structure of phyllosphere microbiome. We analyzed 188 A.thaliana and their phyllosphere microbiome data, identified the hub microbes under four relationships, and screened 622 significant SNP loci. By Bayesian genetic network, 26 hub genes were excavated, which involved in molecular pathways related to plant disease resistance, hormone secretion, and growth and development. This study explored the genetic mechanism of plant regulation of its own microbiome from a genome-wide perspective and revealed how plants and microbiome interacted to promote plant health. It will provide theoretical basis and genetic resources for precision molecular breeding, and support the use of synthetic communities to create new bacterial agents, containing important scientific significance and application value.