This paper presents an analysis on China’s innovative education reform in the tertiary science education from the background of a top-down innovative campaign to its purposes, reasons, effects and challenges. Under the heading of innovation and entrepreneurship education, changes happen in perspectives of educational ideology and practice, involving a wide range of policy backups, learning modes, curriculum reconstruction, teaching ability building, and entrepreneurship supervision improvement, etc. Conclusions show that the top-down innovation campaign is changing the old fabric of knowledge and skill based teaching and learning mode into a practice and innovation based teaching and learning reform. Students and teachers can enjoy a group of stimulant policies, from workload accounting of academic advisors to awarded credits for traditional courses, from scholarship recommendation and quality evaluation to postgraduate selection, from exempting learning and assessment to IE credit replacement, together with the overall arrangement of talent training. However, challenges come from curriculum reconstruction, interdisciplinary cooperation, teaching contents and pedagogy, which reflects the drawbacks of a top-down model of innovation.