It is important to evaluate the independent innovation capacity of high-tech industry scientifically, which could accelerate high-tech industry to become the main body of regional economy. In this paper the evaluation indicators of the independent innovation capacity of high-tech industry are reduced with the distinction matrix algorithm of the attribute reduction based on rough set theory. And then, projection pursuit model method based on genetic algorithms is used to get the synthetic evaluation. High-tech industry of Henan province as a specific example is given according to the evaluation index system with 4 primary indicators and 12 secondary indicators for independent innovation capability. It is proved that the evaluation method is feasible and effective.