In recent years，the funding scale that government invests in TCM colleges increases year by year, but most universities lack of necessary performance evaluation awareness, which severely restricts the best use of funding, Therefore, how to improve the efficiency of medical colleges on education funding has become the focus of many colleges and universities. Performance evaluation on funding should include personnel training, scientific research and social service. The paper measures different kinds of efficiency on education funding in 23 colleges; and analyzes the relationship of non-DEA effective DMU with regional advantages, school ranking and so on, to give some advice to optimize the allocation of educational resources and improve the efficiency of funding.