Tomato yields are reduced under waterlogging and high temperature stress condition. Ascorbic acid (ASA) was shown to be involved in tolerance to waterlogging and heat stresses in tomato. Among 44 wild tomato lines treated with waterlogging at 38°C, L6138 (Solanum peruvianum) showed highest ASA, shoot growth, chlorophyll content and chlorophyll fluorescence in comparison to other tomato lines. Further leaf proteins in L6138 and L0994 under waterlogging at 38°C for 72 h were analyzed by two-dimensional protein fractionation system. Different protein peaks were analyzed by comparative proteomic analysis and database searching. Fifty protein peaks expressed in response to stress treatment were identified, among which 27 proteins from L0994 and 17 proteins from L6138 were successfully sequenced. Differentially proteins expressed have major functions in protein structure maintenance, metabolism, secretion, translation, biosynthesis, signal transduction, degradation, and photosynthesis under stress. ASA might be played a role in tolerance to waterlogging and heat stress by maintaining RNA transcription, protein structure, and metabolism. In this study, we utilized a physiological and proteomic approach to discover the changes in protein expression profiles of tomatoes in response to heat and flood stresses.