In this study, full-length transcriptome sequencing was performed to investigate the activation of IL-2 on flounder lymphocytes in vitro, the related immune pathways in lymphocytes after IL-2 stimualtion were analyzed, and the effects of IL-2 on the proliferation and phagocytosis of B cells after IL-2 receptors blocked were investigated. The sequencing data qualitative analysis showed that a total of 34,519 nonredundant full-length transcripts were generated, 15,507 new transcripts were discovered and 12,416 novel transcripts were successfully annotated. After IL-2 stimulation, 669 genes were upregulated and 740 genes were downregulated in lymphocytes. KEGG analysis showed that the differentially expressed genes in these modules enriched in cytokine-cytokine receptor interaction, MAPK signaling pathway, phagosome, and intestinal immune network for IgA production.