To evaluate objectively the efficiency condition of Knowledge Supply Chain (KSC) is conductive to promoting regional sustained and healthy development of hi-tech industries. Through using KSC theory, DEA model, cluster analysis method, this paper constructs a set of relatively systematic classified evaluation system of KSC efficiency in regard to regional hi-tech industries. Based on the statistical data of China’s hi-tech industries’ statistical yearbook (2013-2014), from the perspective of input and output, classified evaluation results and optimizing countermeasures for China’s 31 provinces and cities’ KSC efficiency in regard to regional hi-tech industries are provided in this paper. The study shows that the KSC efficiency of China’s hi-tech industry is generally quite good. However, great disparities exist for different scales of KSC input and output when comparing hi-tech industries in different types of provinces and cities. Eliminating the waste of input resource, enhancing the amount of efficient invention patents and the sales revenue of new products are main points to improve KSC efficiency of hi-tech industries in backward provinces and cities. The results of this study provide some practical enlightenments for different types of provinces and cities in improving KSC efficiency of hi-tech industries.