Knowledge of heat-tolerant/sensitive cultivars based on morpho-physiological indicators and an understanding of the action and interaction of different genes in the molecular network are critical for genetic improvement. To screen these indicators, the physiological performance of two different varieties of white and red cabbages (B. oleracea var. capitate f. alba and f. rubra, respectively) under heat stress (HS) and non-stress (NS) was evaluated. Cultivars that showed considerable cell membrane thermostability and less reduction in chlorophyll content with better head formation were categorized as the heat-tolerant cultivars (HTC), while those with reduction in stomatal conductance, higher reduction incurred in chlorophyll and damage to thylakoid membranes are categorized as the heat-sensitive cultivars (HSC). Expression profiling of key genes in the HS response network, including BoHSP70 (HEAT SHOCK PROTEIN 70), BoSCL13 (SCARECROW-LIKE 13) and BoDPB3-1 (transcriptional regulator DNA POLYMERASE II SUBUNIT B3-1 (DPB3-1))/NUCLEAR FACTOR Y SUBUNIT C10 (NF-YC10), were evaluated in all cultivars under HS compared to NS plants, which showed their potential as molecular indicators to differentiate HTC from HSC. Based on the results, the morphophysiological and molecular indicators are applicable to cabbage cultivars for differentiating HTC from HSC, and potential target genes for genome editing were identified for enhancing food security in the warmer regions of the world.