Abiotic stress, primarily drought, is a major threat to crop production and food security. Plant metabolites like melatonin and myoinositol enhance stress resistance, improve growth, and promote sustainability without harming biodiversity or human health. Apple farming is crucial to the Himalayan region's economy in India. Despite using High-Density Planting (HDP) with dwarf rootstocks for better yields, these rootstocks are still sensitive to drought, impacting fruit quality and production. To address these challenges, the experiment applied exogenous melatonin (100 µM) and myoinositol (20 µM, 50 µM, 100 µM, 150 µM, 200 µM) to determine optimal doses for biochemical, morphological, and molecular studies. Five apple rootstocks were grown under polycarbonate conditions at 100% and 50% field capacities. Five treatment combinations were tested at 50% F.C., with one control at 100% F.C. Data were collected on the 5th, 10th, and 15th days of drought. The best treatment was melatonin (100 µM) + myoinositol (150 µM) (T4) at 50% F.C., showing the highest net photosynthetic rate (Pn), transpiration rate (Tr), stomatal conductance (Gs) and intercellular CO₂ (Ci) at the 5^th , 10^th and 15^th day of drought for rootstock M111 (15.55, 14.44, 12.65 Pn), (0.21, 0.18 ,0.16 Gs), (267, 278, 287 Ci), M106 (12.81 ,11.96 ,10.86 Pn), (0.17, 0.15, 0.14 Gs), (280, 298, 310 Ci), M9 (10.45 ,9.87 ,8.56 Pn) , (0.17, 0.15 ,0.13 Gs), (327, 332, 339 Ci), Bud 118 (16.78, 14.15, 13.98 Pn), (.26, .24, .23 Gs), (279, 282, 287 Ci), and M116 (13.23, 12.55, 11.53 Pn) , (.21, .19, .18 Gs), (299 ,308, 318 Ci ). Hence, the best treatment combination effectively counteracts drought-related photosynthesis inhibition.