On　the　basis　of　initial　Grey　Target　Theory,　an　improved　grey　target　algorithm　is　applied　for　evaluating　the　regional　independent　innovation　efficiency　in　this　paper.　Benefit　index　is　considered　as　output,　and　cost　index　is　considered　as　input,　the　benefit　euclidean　space　and　the　cost　euclidean　space　are　defined　according　to　different　indexes.　Each　sub-euclidean　space　is　considered　as　a　grey　target,　which　can　be　used　for　evaluating　the　efficiency　by　the　＇bull＇s-eye　distance＇.　Contribution　Degree　Theory　is　applied　for　calculating　the　contribution　degree　of　various　influencing　factors　to　identify　the　key　factors.　Evaluating　results　of　the　regional　independent　innovation　efficiency　demonstrate　that　these　algorithms　are　rational　and　provide　scientific　basis　for　setting　down　new　policies　to　promote　regional　independent　innovation.　©2009　IEEE.