Os11g39000 is a member of atypical bHLH transcription factor family in rice, and its function remains unclear. Yeast two-hybrid experiments revealed that the transcription factor Os11g39000 could form a homologous protein polymer. Random binding site selection demonstrated that Os11g39000 could bind to DNA, and its binding site was preliminarily identified as TT/CG/CACC/GT/C. Expression pattern analysis discovered that the Os11g39000 gene was mainly expressed in leaves and roots, which was a speculation that Os11g39000 may play a role in the developmental regulation of leaves and roots. The hydroponic experiments showed that, compared with wild-type plants, the loss-of-function transgenic plants exhibited much shorter roots and obvious defect in root development, indicating that Os11g39000 was involved in the developmental regulation of roots. Q-PCR analysis further revealed that the transcriptional levels of auxin biosynthesis and signal transduction related genes increased significantly in loss-of-function transgenic plants. These results together demonstrated that the transcription factor Os11g39000 was involved in the regulation of auxin biosynthesis and signal transduction.