With the acceleration of industrialization, the toxic effect of heavy metal cadmium (Cd) pollution has become prominent. In order to explore the molecular mechanism of the physiological regulation of under Cd stress, we analyzed the transcriptome of Cd-stressed (Hcd) algae tissues using RNA-Seq. A total of 702 differentially expressed genes (DEGs) were screened between the control and Hcd groups, out of which 257 genes were up-regulated and 445 genes were down-regulated in the Hcd group. We conducted functional annotation and enrichment analysis of the obtained DEGs. The results showed that various biological functions of were affected under Cdstress, which eventually showed growth inhibition. Results of GO enrichment analysis showed that the production and removal of reactive oxygen species (ROS) in were out of balance and caused oxidative damage such as DNA damage. Results of KEGG enrichment analysis showed that many photosynthesis-related pathways were inhibited, indicating that Cd stress led to disorder of photosynthetic reaction of .