The　embryo　and　endosperm　of　corn　seed　were　analyzed　by　FTIR　spectroscopy.　This　paper　investigated　the　change　of　embryo　and　endosperm　under　the　action　of　microcystins　(MC).　The　characteristic　absorption　peaks　of　embryo　and　endosperm　were　confirmed　and　analyzed　on　spectrum.　The　experimental　evidence　had　shown　that　the　ratio　(I1743:1648)　diminished,　with　the　concentration　of　MC　increased.　In　conclusion,　this　experiment　demonstrated　the　relative　intensity　of　characteristic　absorption　peaks　associated　with　protein　and　lipid　was　altered　by　different　concentrations　of　MC.　©2009　IEEE.