Japan faces the same problem of unbalanced regional distribution of higher education resources as China.By researching the actual situation and the trend of Japanese universities' capacity during the period of 1974 to 2012，the article analyzes the features of universities' capacity in different regions and explores the determinants of the regional difference.The result shows that，wide disparity of higher education scale between large cities and others has existed over a long period.Concretely speaking，as a result of the Japanese higher education policy，the gap of national universities' capacity between regions，except a few large cities，is relatively small.The structural conditions in various regions have little effect on the national universities' capacity.By comparison，the capacity of private universities，affected by social and economic conditions such as personal income，urbanization degree and professional structure，varies greatly between regions.And that is the main reason for the regional difference of Japanese higher education scale.