On　the　basis　of　the　scientific　and　technologic　statistical　data　of　Fujian　province　from　2001　to　2008,　the　present　situation　of　scientific　and　technological　funding　input　was　comprehensively　analyzed,　then　the　optimization　and　configuration　of　scientific　and　technological　funding　input　was　studied　by　Analytic　Hierarchy　Process　and　Grey　System　Theory.　The　result　shows　that　the　grey　relevancy　of　funding　input　and　output　was　the　maximum　for　research　institute　in　different　activity　subjects,　and　was　the　maximum　for　fundamental　research　in　different　activity　types.　So　we　should　optimize　the　funding　input　configuration　in　these　two　aspects　to　get　the　larger　output.　©　2011　IEEE.