Heat stress has deleterious effects on flowering and yield of Tartary buckwheat. In this study, we compared the transcriptomes between thermo-sensitive MQ and adaptive KQ and XQ, in leaves and inflorescences. Compared with adaptive KQ and XQ, flowering genes like FtFT1, FtFT3 and MADS-Box, and developmental genes like PIF3, CIB1, CLAVATA3, YABBY, and HY5 were repressed in thermo-sensitive MQ leaf and inflorescence. Higher proportions of HSPs and HSFs were induced in thermo-sensitive MQ leaf and inflorescence. By using long-read sequencing, we identified DAS events on circadian clock, floral development and heat stress related genes between thermo-sensitive MQ and adaptive XQ. We found the DAS events on PIF, LHY, MADS-Box AGAMOUS and HSF genes generated malfunctional proteins. We speculated that the DAS events on key floral development and heat stress related genes may influence expressions of downstream flowering genes, thus leading to the flowering retardation in thermo-sensitive rice Tartary buckwheat.