In our study, a relatively high concentration of Hg (50 µg/L) was chosen to induce toxicity effect of copepod T. japonicus for 5h. RNA-Seq was performed to determine differentially expressed genes, functional analysis and pathway enrichment analysis of it under control and Hg exposure. The goal of this study is to reveal and compare the molecular resistance mechanisms of T. japonicus response to Hg pollution, and present a new perspective of risk assessment on heavy metal in marine environment.