Filicium decipiens saponin (FDS) is the first saponin purified from F. decipiens seeds using ion-exchange and gel filtration chromatographies. In the present study, FDS and the aqueous crude extract of F. decipiens seeds were examined for their antifungal properties, hemolytic/cytotoxicity activity. The dried seeds were powdered and homogenized in 10% (w/v) for the preparation of crude extract. Sample obtained from Sephadex-LH-20 demonstrated FDS with a peak at 752.35 g/mol. FDS showed the highest toxicity against Aspergillus flavus, presenting with a low fungicidal concentration at 12.8 mu g/mL. Under hemolytic induction, rabbit and cow erythrocytes were more affected by both samples, and the inhibition effect of PpyLL lectin was observed. These characteristics provide fundamental understanding of F. decipiens secondary metabolites, which would benefit future research to prevent dangerous traditional uses and provide agricultural solution.