Chemotaxis-mediated response to root exudates, initiated by sensing-specific ligands through methyl-accepting chemotaxis proteins (MCP), is very important for root colonization and beneficial functions of plant-growth-promoting rhizobacteria (PGPR). Systematic identification of chemoattractants in complex root exudates and their sensing chemoreceptors in PGPR is helpful for enhancing their recruitment and colonization. In this study, 39 chemoattractants and 5 chemorepellents, including amino acids, organic acids, and sugars, were identified from 98 tested components of root exudates for the well-studied PGPR strain Bacillus amyloliquefaciens SQR9. Interestingly, mutant stain SQR9Δ8mcp, with all eight putative chemoreceptors completely deleted, lost the chemotactic responses to those 44 compounds. Gene complementation, chemotaxis assay, and isothermal titration calorimetry analysis revealed that McpA was mainly responsible for sensing organic acids and amino acids, while McpC was mostly for amino acids. These two chemoreceptors may play important roles in the rhizosphere chemotaxis of SQR9. In contrast, the B. amyloliquefaciens-unique chemoreceptor McpR was specifically responsible for arginine, and residues Tyr-78, Thr-131, and Asp-162 were critical for arginine binding. This study not only deepened our insights into PGPR-root interaction but also provided useful information to enhance the rhizosphere chemotaxis mobility and colonization of PGPR, which will promote their application in agricultural production.