Abstract: To promote the rationalization of agricultural production resources allocation and improve the overall operating efficiency of the supply chain, comprehensive evaluation of agricultural product supply chain was carried out. In view of the traditional DEA method ignoring the inner structure of supply chain, a comprehensive efficiency evaluation model based on the typical structure of agricultural supply chain, namely Network DEA model (NDEA), was presented in this paper. And empirical analysis and model application to the present situation and problems of agricultural production in Heilongjiang Province from 2010 to 2012 were conducted. The results showed that the NDEA model was more efficient and could give more information and more reasonable evaluation results comparing with the traditional DEA method. The evaluation model was more in line with the network structure characteristics of the supply chain and the collaboration relationship among individuals, and could analyze the specific inefficient areas in the supply chain. This model provided scientific basis and decision-making reference for optimizing the allocation of resources and improving the overall efficiency and could improve the effectiveness and reliability of evaluation.