Copper (Cu) is one of the essential microelements for plants and algae. It can stimulate growth and photosynthesis at low concentration but inhibit them at higher concentration. The knowledge of molecular response mechanisms to copper stress in green algae is still limited. The responses of the green algae Dunaliella salina to Cu stress were studied using the physiochemical indexes and RNA-seq analysis. The physiochemical indexes such as growth rate, the content of chlorophyll and soluble sugar, photosynthesis and peroxidase activity were all changed in D. salina under Cu stress. In addition, a total of 3799 differentially expressed genes (DEGs) were identified between the control and Cu-treated group. Among these, 2350 unigenes were up-regulated whereas 1449 were down-regulated. Here, the DEGs encoding proteins relevant to photosynthesis, carbon assimilation and carbohydrate mechanism were significantly up-regulated in the Cu-treated group. In addition, the unigenes encoding proteins involved in the antioxidant system and heat shock proteins were also up-regulated, and these were consistent with the expression patterns based on TPM (transcripts per million) values. This study shows that the enhanced growth and photosynthesis and carbon mechanism in D. salina can be triggered by copper, which will lay a firm foundation for future breeding and carotenoid production, further highlighting the underlying application of D. salina as a functional food.