Plants can detect the quorum sensing (QS) signaling molecules of microorganisms, such as amino acids, fat derivatives, and diketopiperazines (DKPs), thus allowing the exchange information to promote plant growth and development. Here, we evaluated the effects of 12 synthesized DKPs on Arabidopsis thaliana roots and studied their underlying mechanisms of action. Results showed that, as QS signal molecules, the DKPs promoted lateral root development and root hair formation in Arabidopsis thaliana to differing degrees. The DKPs enhanced the polar transport of the plant hormone auxin from the shoot to root and triggered the auxin-responsive protein IAA7/17 to decrease the auxin response factor (ARF), leading to the accumulation of auxin at the root tip and accelerated root growth. In addition, the DKPs induced the development of lateral roots and root hair in the Arabidopsis thaliana root system architecture via interference with auxin receptor transporter inhibitor response protein 1 (TIR1). A series of TIR1 sites that potentially interact with DKPs were also predicted using molecular docking analysis. Mutations of these sites inhibited the phosphorylation of TIR1 after DKP treatment, thereby inhibiting lateral root formation, especially TIR1-1 site. This study identified several DKP signal molecules in the QS system that can promote the expression of auxin response factors ARF7/19 via interactions of TIR1 and IAA7/17 proteins, thus promoting plant growth and development.