During the period of Republic of China, the development of national universities can be classified into four periods——the period of slow growth (1912-1921), the period of the rapid expansion (1922-1926), the period of systematization (1927-1936), and the period of steady growth (1937-1949). Meanwhile, the regional distribution of the national universities underwent four stages——the stage of serious imbalance (1912-1926), the stage of relative unbalance (1927-1936), the stage of decentralized(1937-1945), the stage of relative balance(1946-1949). National universities were the carrier of the central ideology and also a tool in the struggle of the parties. The distributional imbalance of national universities was the result of a natural development while the distribution equilibrium was the result of an artificial regulation. There is a historical paradox in the relationship between government and universities. As the crystallization of the fusion between Chinese and Western cultures, national universities were a typical representative of modernization of Chinese higher education.