Abstract Background The Antarctic krill, Euphausia superba (E. superba), is a key organism in the Antarctic marine ecosystem and has been widely studied. However, there is a lack of transcriptome data focusing on temperature responses. Methods In this study, we performed transcriptome sequencing of E. superba samples exposed to three different temperatures: −1.19 °C (low temperature, LT), − 0.37 °C (medium temperature, MT), and 3 °C (high temperature, HT). Results Illumina sequencing generated 772,109,224 clean reads from the three temperature groups. In total, 1,623, 142, and 842 genes were differentially expressed in MT versus LT, HT versus LT, and HT versus MT, respectively. Moreover, Kyoto Encyclopedia of Genes and Genomes analysis revealed that these differentially expressed genes were mainly involved in the Hippo signaling pathway, MAPK signaling pathway, and Toll−like receptor signaling pathway. Quantitative reverse-transcription PCR revealed that ESG037073 expression was significantly upregulated in the MT group compared with the LT group, and ESG037998 expression was significantly higher in the HT group than in the LT group. Conclusions This is the first transcriptome analysis of E. superba exposed to three different temperatures. Our results provide valuable resources for further studies on the molecular mechanisms underlying temperature adaptation in E. superba.