Investment in basic research and operation expenses improves the scale of the scientific research funds for the colleges, how to use research funds reasonably and effectively has a great significance on the university’s research and development. From the perspective of resource efficiency, seven science and engineering colleges are selected to establish an index system, the relative effectiveness is calculated and achievements of scientific research are evaluated for those colleges with the funds in the year of 2003-2008 using Principal Component Analysis(PCA)-Data Envelopment Analysis(DEA) approach, the result provides some recommendations for the use of basic research and operation expenses.