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The leaves of Emmenopterys henryi Oliv. cultured under 25°C/20°C (CK) and 42◦C/37◦C (heat stress, HS), respectively, were used for physiological and transcriptomic analysis based on RNA-seq technology. Results showed that net photosynthesis rate (PN), ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) activity, chlorophyll and brassinosteroid (BR) content, and leaf angle (LA) decreased significantly while the contents of H2O2, thiobarbituric acid reactive substance (TBARS), abscisic acid (ABA) and anthocyanin, and the activities of superoxide dismutase (SOD), catalase (CAT), guajacol-dependent peroxidase (POD), ascorbate peroxidase (APX) increased obviously under HS. RNA-seq analysis indicated that 9492 differentially expressed genes (DEGs) were found, of which 4368 were up-regulated and 5124 were down-regulated. The most enriched KEGG pathways of DEGs were photosynthesis, plant hormone signal transduction, secondary metabolites biosynthesis. HSPs, SOD, CAT, POD, APX were up-regulated whereas genes related to photosystem I (PSI) and photosystem II (PSII) light-harvesting complex and reaction center proteins, cytochrome b6-f complex, plastocyanin, ATP synthase, Rubisco, Rubiscoactivase (RCA), and chlorophyll biosynthesis were down-regulated under heat stress. HS resulted in downregulation of genes related to BR biosynthesis and positive regulation in BR signaling but upregulation of genes related to inactivation of BR. Anthocyanin accumulation in E. henryi under HS might resulted from upregulation of PAL, CHI, DFR whereas downregulation of ANR and LAR. HS led to increase of ABA level but downregulation of genes related to ABA signaling. Transcription factors HSFA, HSFB and HSFC were involved in E. henryi HS response. E. henryi might responds to HS via regulating photosynthesis, antioxidase activity, ABA and BR metabolism and signaling, anthocyanin metabolism and HSPs and HSFs expression. [ABSTRACT FROM AUTHOR]