Abstract: Base on the data of different types of universities during the period of 1999-2011 the scientific and technology innovation efficiency was analyzed by using DEA. The results are as follows. The scientific and technology innovation efficiency is different among various types of universities. Technical efficiency of engineering universities is the highest, and technical efficiency of agricultural and forestry universities is the lowest. The fluctuation of technical efficiency of comprehensive universities, engineering universities, agriculture and forestry universities, normal universities and other universities is mainly caused by the change of pure technical efficiency. Technical efficiency of medical universities is restricted by scale efficiency. RD investment, government support, basic research investment, social service ability, professional and technical personnel had different impact on science and technology innovation efficiency of different types of colleges and universities