Brassinosteroids (BRs) are a class of steroid phytohormones that play diverse roles in plant growth and development and stress responses. Rapid progresses have been made in how BRs regulate plant growth and development in recent years. However, the roles of BRs in stress response in Oryza sativa remain unclear. Here, we investigated the relation between salinity stress and BR synthesis in rice. Both salt stress and abscisic acid, the well-known stress hormone, strongly inhibited the expression of two BR-synthetic genes, D2 and D11. In addition, both d2-2, the BR synthetic mutant, and d61-1, the BR receptor mutant, showed impaired tolerance to salt stress. Moreover, by using transgenic plants overexpressing OsBZR1, the key BR signaling transcriptional factor, we found that BRs strongly induced dephosphorylation of OsBZR1, but high concentrations of salt suppressed OsBZR1 protein accumulation as well as its dephosphorylation. Furthermore, transcriptome analyses revealed that 38.4% of BR-regulated genes were also regulated by high concentrations of salt, and importantly, 91.5% of the co-regulated genes are consistently up- or downregulated by both BR and salt. Gene Ontology analyses revealed that these overlapping genes were highly enriched in the biological process “response to stimulus”. Taken together, our results suggest that BRs contribute to salt stress tolerance, and salt stress suppresses BR synthesis to restrict rice growth.