In this study, we conducted GWAS analyses on three agronomic traits and root microbiota in foxtail millet, a resilient crop against environmental factors. From the 827 cultivars, we identified 33 genetic variations and 131 microbial biomarkers associated with the agronomic traits. Promoting or suppressing effects on foxtail millet growth were further validated by isolated marker strains from field and inoculation experiment in gnotobiotic growth condition. The different marker strains colonized on the root significantly altered the expression of host plant genes with functions related to plant metabolites, nutrient transport, hormone metabolism and immunity response. But plant growth mechanism mediated by microorganisms varied according to the specificity of strains. The core microbiota composition was mainly droved by the genetic variations in genes related to immunity, plant specialized metabolites, hormone signal transductions and nutrition uptake. Our data demonstrated genomic variation-determined root microbiota greatly contribute to crop yield, opening a new way to breed high-yielding cultivars through microbial adaption.