The purpose of this study is to explore the relevance of the notional innovation policy with fuel cell industry of Taiwan. The study also explored the most important factors by literature review, and based on the notional innovation framework by Rothwell & Zegveld’s to find the key factors of national innovation policy of Taiwan’s fuel cell energy industry. The process of research did the literature review and collected secondary data and data analysis, then measured and analyzed the outcome through AHP (Analytic Hierarchy Process) method. The research concluded the priority policy of demand and supply side affected the Fuel cell industry. And the considerable factors of “Subsidized policies”, “Innovation incubation policies” and “Government procurement policies” were the three most important factors to national innovation policy of Taiwan’s Fuel Cell industry. Furthermore, the research according to the outcome obtained the suggestions to fuel cell industry innovational policy.