High temperature reduces the growth and yield of most of the agriculturally important crops. Elicitors have been reported to modulate the thermotolerance of crops under abiotic stresses. Here, we studied the effect of salicylic acid (SA) on thermotolerance level of C306 (thermotolerant) and PBW343 (thermosusceptible) wheat cultivars grown under heat stress. Pilot experiment confirmed spraying of 100 mM SA prior to heat stress (38 °C, 2 h) as the most effective treatment. Numerous protein spots were observed in C306 under SA + HS compared to PBW343 during post-anthesis stage by 2-DE. Differentially expressed proteins were identified as signaling molecule, heat-responsive transcription factors (HSFs) and heat shock proteins (HSPs) using MALDI-TOF–TOF/MS analysis. Abundance of transcripts of HSFs, HSPs, CDPK, SOD, RCA, etc. was observed in C306 in response to SA + HS, as compared to PBW343. C306 showed better accumulation of transcript of SAGs, osmolyte and total antioxidant capacity under SA treatment compared to PBW343. SA was observed to reduce the detrimental effect of HS on soluble starch synthase (SSS) activity as well as synthesis of starch granules in both the cultivars.