Microorganisms have established a beneficial relationship with the plants by secreting auxin and auxin precursors and alter plants root system architecture. Moreover, other metabolites are secreted by microorganisms can also change the plant auxin signaling pathway. Thus, auxin and auxin signaling pathways play an important role during the process of microbes modulate plant root development. This review summarizes the role of auxin during the process of microorganism regulate the development of plant root system from auxin synthesis, auxin signal and auxin polar transport, including microorganism increase the content of plant endogenous auxin, enhance the signal of auxin and regulate the expression level of PIN protein. Further, we concluded how microorganism regulated plant physiological and molecular level to adapt the changes of root system, which laid the foundation for further research in this field.