Dormancy is a fascinating survival technique that enables organisms to adapt to their environment and can be classified as either hibernation or aestivation, depending on the season. Organisms that are in a state of dormancy can display remarkable stress resistance, enabling them to survive in extreme environments. However, the question of how organisms adapt to their environment in their respective dormant states and how the two types of dormancy relate to each other and differ from each other still deserves further exploration. We selected Perccottus glenii and Protopterus annectens as the primary subjects to study hibernation and aestivation respectively. We analyzed them histologically and collected multiple organ transcriptome data from both species. The functional enrichment results reveal that dormancy entails a comprehensive alteration coordinated by multiple organs. Additionally, the differences between the two dormant species (regarding coping mechanisms to deal with extreme temperatures) were considerable. We also discovered noteworthy similarities in the expression patterns of genes linked to energy metabolism, neural activity, and biosynthesis during both dormant periods, indicating a correlation between hibernation and aestivation. To comprehend the connection between the two dormant species, we scrutinised the gene homology of various other distantly related species in dormant states from public databases. We discovered that almost half of the directly homologous genes showing significant differential expression during dormancy displayed a consistent expression trend. These genes, which exhibit similar expression patterns, mainly regulate metabolism during dormancy, and maintaining the biologically dormant state requires cell number and neural activity. This suggests that the similarity between hibernation and aestivation is due to convergent evolution. In conclusion, our study enhances the comprehension of the dormancy phenomenon and offers new insights into the molecular mechanisms behind vertebrate dormancy.