Abstract: Large and medium-sized industrial enterprises are the innovative subject of building innovation country and the backbone of the progress of innovation-driven. The regional gap of its innovation capability will affect the coordinated development of regional economy. This article, employing the method of improved TOPSIS and the model of Theil entropy, measures the regional gaps of innovation capabilities of large and medium-sized industrial enterprises, based on the panel data of 30 provinces, municipalities and autonomous regions in Chinese mainland from 1999 to 2010.The results show that the gaps of the innovation capabilities of large and medium-sized industrial enterprises between different regions in China are large, and furthermore, the gaps reveal expanding tendency. As for the regional internal differences, the innovation capability gap of the southeast, southwest and northwest regions are large and the Yangtze River Delta and central regions are small. Moreover, this article illustrates that the disparities between different regions are the prior factor influencing the innovation capabilities of large and medium-sized industrial enterprises, while the internal differences of different regions have less impacts. The results of this study could play an important role in guiding the policies aiming to narrow regional gaps and promote development of large and medium-sized industrial enterprises.