FTY720 is a synthetic compound derived from the metabolites of Isaria sinclairii. Its unique chemical structure and mechanism appear to be distinctive from other known immunosuppressors. In the present study, the effect of FTY720 on immunosuppression and toxicity to heart was evaluated by detection of lymphocytes count, heart rate in rats, the survival time of the allografts of skin slice in mice and binding to S1P1 and S1P3 receptors by confocal. The results showed that FTY720 could induce lymphopenia, reduce the heart rates in rats and prolong the survival time of the allografts of skin slice in mice. The assay results on confocal showed that FTY720 can bind with S1P1 and S1P3 on surface of CHO-S1P1 and CHO-S1P3 cells. FTY720 could be developed for wide application for organ transplantation and self-immunity diseases.