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Calcium acts as a signaling molecule and plays very important role in plants-tolerance to the abiotic stresses including the heat stress. We studied the effect of exogenous Ca2+ (10 mM) prior to the heat stress (42 °C, 2 h) on different molecular and biochemical parameters associated with thermotolerance in wheat (Triticum aestivum). We could observe 64 and 52 unique protein spots in HD2967 (thermotolerant) and HD2329 (thermosusceptible) cultivars under normal and heat stress condition. Similarly, 13 and 9 (HD2967) and 19 and 9 proteins (HD2329) were observed to be up-regulated and down-regulated in response to HS. MALDI-TOF-TOF/MS characterization identified the differentially expressed protein (DEP) spots as calcium dependent protein kinase (CDPK), oxygen evolving enhancer protein, HSP17, HSP70, Rubisco activase etc. Transcript profiling of identified stress-associated genes (SAGs) showed very high expression of CDPK, HSFA4a, HSP17, SOD and APX in response to Ca2+ + HS in HD2967 compared to HD2329 cultivars of wheat. Similarly accumulation of signaling molecules (H2O2 and CDPK) as well as osmolyte was observed maximum in response to Ca2+ + HS in HD2967 compared to HD2329 cultivars. Very high activities of guaiacol-peroxidase and ascorbate peroxidase were observed in Ca-treated HD2967 compared to HD2329 when exposed to HS. It is the abundance of these chaperones and antioxidant enzymes in thermotolerant cultivar which limit the accumulation of H2O2 in response to Ca2+ and HS. Exogenous Ca2+ application showed negative correlation with lipid peroxidation and positive correlation with total antioxidant capacity of the cell system under the elevated temperature. Alteration in Ca2+ efflux triggers the activities of kinases and peroxidases more in tolerant compared to susceptible cultivars which regulate the accumulation of ROS inside the cell and attenuate the lipid peroxidation process. Ultimately, it enhances the total antioxidant capacity and thermotolerance of the plants under the heat stress.