Abstract：Based on a set of evaluating index system and using synthetically evaluating method of factor analysis and spatially varying-coefficient econometric analysis model, the clustering and difference together with its relationship between Regional Innovation Milieu (RIM) and University Knowledge Innovation Capability (UKIC) in 31 Chinese provinces are analyzed. The results show that (1) factor analysis and spatially varying-coefficient econometric analysis models have good effects on the synthetic evaluation and spatial correlation analysis of regional RIM and UKIC; (2) there are obviously local clustering and significant difference between RIM and UKIC of Chinese provinces；(3) the spatially positive effects of RIM on UKIC are locally significant and robust, and the favorable innovation milieu is in favor of the formation of UKIC. Only the institutional arrangement of difference and heterogeneity together with the innovation milieu of regional characteristic, exerting resources advantage, and favoring competition-cooperation can promote the contribution of UKIC to regional innovation capability to the maximum.