Abstract:With Chinese economy entering the new normal era, the national independent innovation demonstration zones have become the important growth poles for China's implementation of the innovation-driven development strategy.Because the national independent innovation demonstration zones maintain a relatively rapid development speed by promoting entrepreneurial employment and speeding up the transformation of innovative achievements into real productivity. Papers from the input and output efficiency of science and technology innovation, to construct the evaluation index system of innovation ability of national independent innovation demonstration zone, the indexes are classified according to the character of input and output and processes it by factor analysis method,finally using cross DEA model to evaluate the scientific and technological innovation efficiency of six high-tech development zones in Shandong Peninsula National Independent Innovation Demonstration Zone. It is concluded that the efficiency of Shandong Peninsula National Independent Innovation Demonstration Zone is effective, but the level of cross-efficiency is still at the middle level. The efficiency of innovation still needs to be further improved.