This paper described the geometric structure of panel data's curved surface in 3D space, and established the synthesized similarity index for the curved surface through several aspects including the absolute magnitude, growth rate, geometric similarity and spatial absolute distance. The traditional fuzzy C-means clustering method was optimized through replacing the distance with the similarity index. On this basis, this paper explored the patent out put type characteristic and the rule of its territorial differentiation in China's 31 provinces (municipalities) during the years of 2000-2010. The empirical results showed that the clustering effect was good, and Chinese patent output showed an upward trend and spatial heterogeneity and autocorrelation generally at the same time no matter in the number, the performance or the growth rate. The innovation capability of more and more regions in central and western China were getting enhanced, although regions with higher innovation ability still concentrated in the eastern China. In addition, the boost of innovation mainly came from governments5 promotion especially the R&D funding investment, however, the allocation of R&D resources and the personnel disposable funds were both extremely unbalanced among regions. Besides, there were distinct differences in the innovation efficiency between eastern and western regions for the financial allocation from government. The government should formulate a reasonable regional scientific and technological development strategy and sets of policy tools according to the regional R&D ability and resource endowment, so as to exploit the regional motivation power of innovation and to improve regional patent innovation capability. [ABSTRACT FROM AUTHOR]