In the past, the president of a national university in Taiwan is designated by the central government; however, the call for the university president electing system is surging higher and higher due to the heavy backlash to the existing designation system, the change of the political and social atmosphere and the well-discussed and resounding concept that university should be dominate by the faculty. At the end of 1993, the University Law is validated, and the president creating system is therefore changed form the designated to the elected system. As a leader of a university, a president is responsible for most of the operating efficiency of the university. The president who is designated by the Ministry of Education acquires his power from the central government and therefore tends to put more stress on his relationship with the authorities instead of the management of the university; on the contrary, the elected president will tend to pay more attention to the internal affairs of the university, for his power comes from the recognition of each members in the university. Hence, in this paper we suggest that the difference between the two president creation systems will significantly affect the president’s priority on which field to put more emphasis, and furthermore cause different effects on the operating efficiency of a university. The main purpose of this research is to evaluate the influence over the operating efficiency of a university form the president designating system to the president electing system. Because a university has the properties of multiple inputs and outputs and is a not-for-profit institution, in this paper we use the Data Envelopment Analysis and the Regression Analysis to verify the above empirical hypothesis. This paper is the first one to use actual operating data to test the above empirical hypothesis. The empirical results reveals that, after the change of president creating system for the designated to the elected, the operation efficiencies of the national universities are significantly increased. That is, the president electing system has a significant and positive effect on the operating efficiencies of the national universities in Taiwan.