This article using data envelopment analysis to evaluate the operating efficiency of 29 private universities from 2001 to 2005 in Taiwan. We making the efficiency to be a Panel data form, and then using the Panel Tobit model to analysis the efficiency of DMU from exogenous variables. This article emphasizing to solve the time series periods which not long enough in Panel data. From the average of technical efficiency, pure technical efficiency and scale efficiency, we can prove that 29 DMU’s up increasing in this periods. From the pure technical efficiency analysis, there are 7 DMUs to be 1 in every year, it involving TKU, PCCU, TTU, USC, FCU, HCU and TOKO. We can see that the established periods is shorter on HCU and TOKO, it can prove that the efficiency is independent of establishment periods of school. When using Panel Tobit model to analysis the effect of environment variables to efficiency of school, we can prove that the DMU’s efficiency are not affecting by established periods and the school whether or not in the city, but it can be affect by the region of the DMU.