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A performance evaluation model based on DEA with worst decision-making units is constructed, which meets the need of the performance evaluation of systems engineering with a number of similar samples, multi-input and multi-output. It achieves the goal of making total order for the objective evaluation of the decision-making assessment. Potential to influence decision-making units of the system point of view have been proposed, based on the DEA model to basically achieve the objective comparison of various decision-making units. The effective decision-making unit of the system leading to the potential losses based on DEA are taken into account. Because the DEA (CCR) with weak efficient decision making units leads to that the potential loss of value are zero for the system, we set the worst decision-making units corresponding to these DMUs e-evaluation based on the DEA model. Finally, by utilizing model to the practical cost-effectiveness evaluation of 15 institutions of higher education in Henan province, the advantages of the whole evaluation and decision in this model are shown.