An understanding of the molecular mechanisms underlying temperature-dependent responses in microorganisms is essential to elucidate their adaptation mechanisms to environmental changes. In this study, we investigated temperature-dependent gene expression profiles of Chlorella strains by detailed analysis of differentially expressed genes (DEGs) and gene ontology (GO) functions. They reveal significant variation in gene expression under different temperature conditions. Surprisingly, ribosomal RNA modification, script digestion, DNA replica, carbohydrate and stress liability generation are revealed by discriminative syllables, which revealed the genetic processes of the inflammation. They continue to meet or exceed the comparison, whereby their conserved transcriptional responses indicated to temperature change. These results provide valuable insights into the molecular mechanisms regulating adaptation to temperature change and a basis for further research on regulatory interactions and signaling pathways involved in temperature-mediated gene expression including biofuel production and environmental production.