Abstract: The innovation ability of 12 representative cities in the east of China has been analyzed by the method of gray cluster analysis from the four respects of knowledge technology, system and service innovation abilities as well as the city macroscopic development level. The analyzed results can be classified into three kinds: The first kind of cities have the strongest innovation ability superior to other cities in various respects; The second kind cities have relatively strong innovation ability in totality, but are weak in some fields. That need to strengthen the establishment of innovation system and innovation strategy so as to tackle the problems; The third kind of cities are weakest in innovation ability, which must enhance the innovation ability in all respects.