High temperatures cause physiological and biochemical changes and significantly affect young panicle development of rice (Oryza sativa L.). Brassinosteroids play important roles in enhancing crop stress resistance. In this study, we subjected rice cultivars Huanghuazhan (heat-resistant) and IR36 (heat-sensitive) to high temperature (HT, 40 oC) or normal temperature (NT, 33 oC) for 7 d at the panicle initiation stage, in conjunction with application of 24-epibrassinolide [EBR, a synthetic brassinolide (BR)] or brassinazole (BRZ, a BR biosynthesis inhibitor) at the beginning of the treatments. HT exacerbated spikelet degeneration and inhibited young panicle growth, which were partially prevented by EBR application, while BRZ application aggravated the reduction in spikelet number. HT decreased the contents of BR, active cytokinins (aCTK), active gibberellins (aGA) and indole-3-acetic acid (IAA), but increased the content of abscisic acid (ABA) in young panicles. The activities of key enzymes involved in sucrose hydrolysis, glycolysis and the tricarboxylic acid cycle in young panicles were decreased with the change of endogenous hormone levels under HT. In addition, the contents of H2O2 and malondialdehyde (MDA) were increased and the activities of antioxidant enzymes were decreased in young panicles. Exogenous application of EBR induced the expression of phytohormone biosynthesis-related genes and down-regulated the expression of phytohormone catabolism-related genes to increase the contents of endogenous BR, aCTK, aGA and ABA, thus promoting the decomposition and utilization of sucrose in young panicles, enhancing the activities of superoxide dismutase, catalase and peroxidase, and reducing the accumulation of H2O2 and MDA in young panicles, whereas application of BRZ had the opposite physiological effects. These results showed that brassinosteroids mediate endogenous phytohormone metabolism to alleviate HT injury at the panicle initiation stage in rice.