High temperature affects yield and quality of vegetable crops. Thermotolerant plants have excellent systems for identifying molecular mechanisms of heat responsive. In this paper, Various heat resistance indexes of thermotolerant (‘14’) and thermosensitive (‘02’) cucumber plants were observed at seedling stage, and the similarities and differences of regulatory genes were detected by transcriptome, so as to provide a train of thought for studying the effects of heat stress on the internal mechanism of cucumber. Leaf orientation, photosystem, water loss, ROS of ‘14’ plants displayed enhancer responsive than that of ‘02’ plants under high temperature. In corresponding, transcriptome analysis shown that genes in photosynthesis, chlorophyll metabolism and water homeostasis were upregulated in ‘14’ plants, but downregulated in ‘02’ plants. The content of ZR, BR and JA of ‘14’ plants was more than that of ‘02’ plants, GA increased in both but higher in ‘14’, IAA and GA were boosted by heat in ‘14’ and ‘02’ after high temperature stress. Further correlation and interaction analysis revealed that a small number of transcription factor family genes and the metabolic pathways corporately regulate heat responsive. Our study revealed different phenotypic and physiological mechanisms of heat response in thermotolerant and thermosensitive cucumber plants, revealed different expression profiles and preference metabolic pathways between thermotolerant and thermosensitive plants. The transcription factors and genes that involved in heat resistance were analyzed comprehensively. Those results enhanced our understanding on the molecular mechanisms of high temperature responsive in cucumber.