Today, growing the production of the agricultural sector in order to meet the increasing demand of food is happening through excessive consumption of water resources, energy, chemical fertilizers, and pesticides, especially in developing countries. Therefore, the present study aims to design a new approach for sustainable management of resources and realization of clean production in the agricultural sector. In order to design the new approach of the present study, the integration of two concepts of water-energy-food (WEF) nexus and decoupling pollution-agricultural growth (DEC) was used. The proposed approach is modeled through the multi-objective programming model by optimizing the WEF and DEC indices, which is the first research effort in this field. In this regard, the performance of this approach was evaluated in Jiroft County in Kerman province, Iran. The results of the study showed that the consumption of chemical fertilizers and pesticides in the optimal pattern with the simultaneous provision of WEF and gross margin (GM) goals (optimal 1) is about 110 kg and 0.19 l per hectare, respectively, more than the proposed pattern (optimal 3). On the other hand, the consumption of water and energy resources in the optimal pattern with the simultaneous provision of DEC and GM goals (optimal 2) is about 8785 cubic meters and 1108 MJ per hectare more than the proposed pattern (optimal 3), respectively. Therefore, this approach, due to the simultaneous integration of two concepts of sustainable development in the agricultural sector, can overcome the weakness of the WEF nexus in not paying attention to the issues of environmental pollution affected by the use of chemical inputs and the weakness of separating pollution-agricultural growth in not paying attention to the management of water and energy resources in the agricultural sector.