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Equipment manufacturing industry is the basic department of national economy and the strategic industry in China. To strengthen the ability of self-innovation and the efficiency of technology innovation is the only way to brace up the equipment manufacturing industry in China. Therefore establishing the evaluation index system of independent Innovation ability of equipment manufacturing industry in China is very meaning for equipment manufacturing enterprise to evaluate well and truly itself, find technological problems and improve innovation capability. In this paper, the independent innovation capability is divided into two parts: innovation input & output and innovation efficiency. Based on the result of evaluation, this paper discovers that the weakness of the self-innovation ability and the lowness of technology innovation efficiency are the bottleneck factor which restricts the development of the equipment manufacturing industry in China.