The impacts of exogenous rosmarinic acid (RA, 100 μM) and/or hesperidin (HP, 100 μM) were evaluated in improving tolerance on the gas exchange, chlorophyll fluorescence and efficiencies, phenomenological fluxes of photosystems, antioxidant system and gene expression related to the lipid biosynthesis under heat stress. For this purpose, Arabidopsis thaliana was grown under RA and HP with heat stress (S, 38 °C) for 24 h(h). As shown in gas exchange parameters, heat stress caused mesophyll efficiency and non-stomatal restrictions. Both alone and combined forms of RA and HP to stress-treated A. thaliana alleviated the disturbance of carbon assimilation, transpiration rate and internal CO2 concentrations. Stress impaired the levels of energy flow reaching reaction centers of PSII and the photon capture ability of active reaction centers. RA and/or HP enhanced photosystems' structural/functional characteristics and photosynthetic performance. Histochemical staining and biochemical analyses revealed that heat stress caused the oxidation in A. thaliana. By activating several defensive mechanisms, RA and/or HP could reverse the harm caused by radical production. Both alone and combined forms of RA and HP removed superoxide anion radical (O2•−) accumulation, inducing superoxide dismutase (SOD). The common enzyme that scavenged hydrogen peroxide (H2O2) at all three applications (S + RA, S + HP and S + RA + HP) was POX. Also, only RA could utilize the ascorbate (AsA) regeneration in response to stress, suggesting increased ascorbate peroxidase (APX), monodehydroascorbate (MDHAR) and dehydroascorbate (DHAR) activities. However, the regeneration/redox state of AsA and glutathione (GSH) did not maintain under S + HP and S + RA + HP. While RA had no positive influence on the saturated fatty acids under stress, HP increased the total saturated fatty acids (primarily palmitic acid). Besides, the combined application of RA + HP effectively created the stress response by increasing the expression of genes involved in fatty acid synthesis. The synergetic interactions of RA and HP could explain the increased levels of saturated fatty acids in combining these compounds. The data obtained from the study will contribute to the responses of phenolic compounds in plants to heat stress.