The worsening water scarcity has imposed a significant stress on food production in many parts of the world. This stress becomes more critical when countries seek self-sufficiency. A literature review shows that food self-sufficiency has not been assessed as the main factor in determining the optimal cultivation patterns. However, food self-sufficiency is one of the main policies of these countries and requires the most attention and concentration. Previous works have focused on the virtual water trade to meet regional food demand and to calculate trade flows. The potential of the trade network can be exploited to improve the cropping pattern to ensure food and water security. To this end, and based on the research gaps mentioned, this study develops a method to link intra-country trade networks, food security, and total water footprints (WFs) to improve food security. The method is applied in Iran, a water-scarce country. The study shows that 781 × 106 m3 of water could be saved by creating a trade network. Results of the balanced trade network are input to a multi-objective optimization model to improve cropping patterns based on the objectives of achieving food security and preventing water crises. The method provides 400 management scenarios to improve cropping patterns considering 51 main crops in Iran. Results show a range of improvements in food security (19-45%) and a decrease in WFs (2-3%). The selected scenario for Iran would reduce the blue water footprint by 1207 × 106 m3, and reduce the cropland area by 19 × 103 ha. This methodology allows decision makers to develop policies that achieve food security under limited water resources in arid and semi-arid regions.