Input-output efficiency of financial research funds in Colleges and universities is an important reference for government financial input.Taking the cross-sectional data of scientific research input and output in Henan Province as an example,this paper uses Data Envelopment Analysis (DEA) model to evaluate the financial input and output efficiency of 21 colleges and universities at different levels. The results show that the input-output efficiency of scientific research in 12 colleges and universities is DEA effective; a weakly effective university have large scale and decrease in scale, and the comprehensive technical efficiency is not optimal;Eight non-DEA effective universities do not achieve the best comprehensive technical efficiency, but they are all in a state of increasing scale. The scale of weakly effective university should not be expanded, but more attention should be paid to the scientific research output and the transformation of achievements; the non-effective universities can increase the scale of scientific research input, improve the incentive mechanism of scientific research, strengthen the talent introduction and actively promote the growth of the research output. The research results can provide useful information for the development of universities and the allocation of government financial research funds.