Since the fifth plenary session of the 16th CCCPC and National Science and Technology Assembly，common sense has been formed in promoting enterprises as the main body of independent innovation and its core competitiveness. There are still lack of scientific evaluation standard and measurement in constructing innovative enterprises and measure and identify innovative enterprises. This paper constructs an enterprise independent innovative capability evaluation indicator system and hierarchy structure model from the aspect of potential innovation resources，innovation input and innovation output，and conducts an empirical evaluation and analysis on innovative index to Guangdong 56 innovation pilot enterprises. Meanwhile，a series of proposals on promoting Guangdong enterprises’ independent innovation capability are also offered.