High light (HL) intensity has a substantial impact on light energy flow and partitioning within photosynthetic apparatus. To realize the impact of HL intensity on zinc (Zn) tolerance mechanisms in clary sage (Salvia sclarea L., Lamiaceae) plants, we examined the effect of the altered chlorophyll and nutrient uptake under excess Zn supply on the response mechanism of photosystem II (PSII) photochemistry. Eight-week-old clary sage plants were treated with 5 μM Zn (control) or 900 μM Zn in Hoagland nutrient solution. Leaf elemental analysis for Zn, Mn, Mg, and Fe was performed by inductively coupled plasma mass spectrometry (ICP-MS), whereas PSII functioning under HL was evaluated by chlorophyll fluorescence imaging analysis. Exposure of S. sclarea plants to 900 μM Zn increased leaf Zn accumulation and decreased leaf Mg and chlorophyll. The decreased non-photochemical quenching (NPQ) provided evidence of the photoprotection offered by the smaller light-harvesting antennae due to the reduced chlorophyll. The increased Mn after Zn exposure corresponded with higher efficiency of the oxygen-evolving complex (OEC) that was significantly correlated with the maximum efficiency of photosystem II (PSII) photochemistry (Fv/Fm). An increased electron transport rate (ETR) coincided with increased leaf Fe, which is known to play a vital role in the enzymes engaged in ETR. The decreased (32%) NPQ after an 8-day exposure to Zn caused an increased (10%) quantum yield of non-regulated energy loss in PSII (ΦNO), indicative of an increased singlet oxygen (1O2) production. It is suggested that the decreased NPQ induced acclimation responses of clary sage plants to HL and excess Zn by increasing 1O2 production. The reduced (18%) excess excitation energy (EXC) at PSII and the increased (24%) quantum yield of PSII photochemistry (ΦPSII) and ETR indicated improved photosynthetic efficiency under excess Zn and HL intensity. Therefore, the exposure of medicinal plants to excess Zn not only boosts their photosynthetic efficiency, enhancing crop yields, but can also improve Fe and Zn content, ameliorating the human health deficiency of these two essential micronutrients.