The development and evolution of regional economic competitiveness is improved during the transformation from efficiency-driven economy to innovation-driven economy, which makes system resources and factor resources concentrate to innovation sectors and has an impact on the pattern of the original regional economy resulting in the fluctuation and risk of regional economy caused by the innovation changes. Essentially, the fluctuation and risk are the costs resulted from the transformation from efficiency-driven economy to innovation-driven economy and reflected in the following respects: the convergence of innovation-driven strategies among regions, the deviation of the endogenous path of innovation, the increasing local economic fluctuations and uncertainties brought by SMEs in innovation.