SUMMARY Salicylic acid (SA) plays important roles in different aspects of plant development, including root growth, where auxin is also a major player by means of its asymmetric distribution. However, the mechanism underlying the effect of SA on the development of rice roots remains poorly understood. Here, we show that SA inhibits rice root growth by interfering with auxin transport associated with the OsPIN3t‐ and clathrin‐mediated gene regulatory network (GRN). SA inhibits root growth as well as Brefeldin A‐sensitive trafficking through a non‐canonical SA signaling mechanism. Transcriptome analysis of rice seedlings treated with SA revealed that the OsPIN3t auxin transporter is at the center of a GRN involving the coat protein clathrin. The root growth and endocytic trafficking in both the pin3t and clathrin heavy chain mutants were SA insensitivity. SA inhibitory effect on the endocytosis of OsPIN3t was dependent on clathrin; however, the root growth and endocytic trafficking mediated by tyrphostin A23 (TyrA23) were independent of the pin3t mutant under SA treatment. These data reveal that SA affects rice root growth through the convergence of transcriptional and non‐SA signaling mechanisms involving OsPIN3t‐mediated auxin transport and clathrin‐mediated trafficking as key components. Significance Statement In this study, we found that salicylic acid (SA) inhibited rice root growth by inhibiting the clathrin‐mediated endocytosis of OsPIN3t with a non‐canonical SA signaling mechanism. Meantime, OsPIN3t was at the center of the gene regulatory network containing clathrin, and the clathrin‐mediated root growth was independent of the OsPIN3t under SA treatment. Our study shows that SA regulated rice root growth by convergence of transcriptional and non‐SA signaling mechanism mediated by the OsPIN3 and clathrin.