Abstract:China is changing from R & D Great Power[ ] to R & D power, which is not the natural process from a quantitative change to the qualitative change. The structural problems of system coupling of government-university-industry in Different Provinces are the fundamental problems to restrict regional innovation system to improve the overall efficiency. This paper adopts the Triple Helix Algorithm to comparatively analysis the structural problems of system coupling of government-university-industry in the 23 provinces of China such as Beijing, Shanghai, Zhejiang etc.on the base of SCI-E database. The results find that the coupling effect of government-university-industry in most provinces is relatively poor, the optimization and structural condition of regional innovation system are unreasonable.