Maintaining a stable basal level of salicylic acid (SA) is crucial for plant growth, development, and stress response, though basal levels of SA vary significantly among plant species. However, the molecular mechanisms by which basal SA regulates plant growth and stress response remain to be elucidated. In this study, we performed a genetic screen to identify suppressors of the root growth defect in Osaim1, a rice mutant deficient in basal SA biosynthesis. We found that mutation in the E3 ligase OsPRT6, a key component of the Arg/N-degron pathway, rescued the root growth defect of Osaim1. Further analysis revealed that OsWRKY62 and OsWRKY76 act as substrates of the OsPRT6 N-degron pathway to modulate root growth. We demonstrated that reducing the basal SA levels activate the PRT6 N-degron pathway. Additionally, we found that basal SA modulates stress response partially through the PRT6 N-degron pathway. Importantly, the effects of basal SA levels on PRT6 N-degron pathway are conserved in plants. Taken together, these findings uncover a novel regulatory mechanism in which the basal SA represses the PRT6 N-degron pathway to modulate root growth and abiotic stress response in rice.