Using the dynamic comprehensive evaluation model, a dynamic evaluation on the independent innovation capacity of high-tech industry in China by region is carried out. So the changing trend of the independent innovation capacity of high-tech industry in each region is obtained, as well as the regional difference. Through the comparative analysis of the evaluation results, those indicators having the relative advantages or having the relative disadvantages in structure of the independent innovation capacity of high-tech industry in each region are defined. As a result, the decision basis for promoting the independent innovation capacity of high-tech industry in China comprehensively is offered by this paper, In addition, the decision provide help for potential risk analysis of high-tech industry in China.