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As military enterprises, aeronautical enterprises are very important to national security. In order to keep strong competitive advantage, these enterprises need to continuously improve their technological innovation. How to evaluate effectively the innovation system is a problem. Firstly, the characteristics of technological innovation for aeronautical enterprise are compared with traditional enterprise. Secondly, with the customer-oriented idea of quality function deployment (QFD), a new evaluation method based on QFD is proposed. Performance index system and customer demand are also given. Meantime, the detailed evaluation steps are represented. Finally, the case study shows the validity of this method.