The evolution of regional innovation is reflected both by the characteristics of convergence or divergence and spatial interdependence respectively from the time and space perspectives. China and Japan is the representative developing country and developed country from Asia and there are many differences on the development modes and evolution features of their regional innovation. As there are few comparative studies on China and Japan’s regional innovation based on convergence and spatial interdependence, patent application amount is adopted, the index of Gini and Moran I is calculated in order to investigate the evolution characteristics on regional innovation of China and Japan in terms of overall regional convergence, intra-regions convergence, and inter-regions convergence, as well as the spatial interdependence of regional innovation.