An efficiency evaluation of inner structure for universities was proposed based on data envelopment analysis (DEA). The operational efficiency of the universities was divided into operational stage and profitability stage. The efficiency of the profitability stage was decomposed into educational and research efficiencies. Both efficiencies were estimated for parallel structure system. To prove the rationality and effectiveness, the case study of a specific 985project university was investigated based on the data of its inner colleges. The method provides more effective operational management suggestions for the universities.