University is the important component of national innovation system of science and technology, and it is the important source of scientific and technological innovation. This paper brings the environment variable by fuzzy number form into the DEA model ,constructs the fuzzy DEA model which is based on the solutions of the cut set method, and makes up the empirical simulation in China. The result proves that the environment factors do have certain effect on the operational efficiency ,and certifies that this model is suitable for the measurement of university of science and technology system.