Abstract: This article establishes a regional innovation strength evaluation index system. Based on the improved normalization method and variation coefficient method, it standardized the data, determined the weight, and used twice-weighted method to calculate the weighted average of the regional innovation strength in 31 Chinese mainland provinces and autonomous regions from 2001 to 2010, thus, to make dynamic evaluation and classification comparative analysis. Viewed from their rankings, the research shows, from 2001 to 2010, the strengths of regional innovation capabilities of the eastern coastal areas are at the highest level, those of the central regions at the middle, and those of the western regions at the lowest. The main reason is the advantage of funding, policy, personnel and innovative carrier in the eastern regions, the constraints of industrial structure, business and innovative ideas in the central, northeast China and the relatively low levels of economy, education and scientific research and so on in the western China. Studies suggest that the weaker regional innovation could be improved through increasing R & D investment, introducing innovative talents, optimizing the industrial structure, and improving innovation support policies to enhance collaborative research innovation means.