A new approach that has dominated the production operations management field in recent years is supply chain management. A supply chain includes all the facilities, tasks and activities involved in manufacturing a product from suppliers to customers. Its various elements are planning, supply and demand management, procurement of raw materials, production scheduling, distribution and delivery of products to the customer. Special structures in the supply chain have been less studied in previous research. In this paper, the supply chain and its performance evaluation are examined in the presence of non-discretionary, undesirable and negative data. For this purpose, another model of the network DEA is presented which evaluates performance of the chain in the presence of non-discretionary inputs and outputs, undesirable outputs and negative outputs even in its internal structure. The efficiency of the chain stages is also calculated using a dual model. Subsequently, 42 cement companies listed on the Tehran stock exchange were evaluated, each of which has a chain of four stages including suppliers, manufacturers, distributors and customers. Based on the implementation of the model, six companies were found to be efficient and the rest were introduced as inefficient. Moreover, 25 cement companies in the Supplier sector, 18 companies in the manufacturing sector, seven companies in the distribution sector and finally 17 companies in the customer service sector were found to be efficient.