Abstract: As an important energy and major grain producing area in China, the Yellow River basin has had a shortage of water resources, becoming a key factor in the restriction of energy and food development. And the system risk of water, energy and food has been escalated. An overall analysis framework model of water-energy-food based on the synergetic theory was established in order to optimize the relationship between water resources, energy, and food. Further, a total partition structure model was built, also known as the water-energy-food collaborative optimization model with an inter-feedback function. The support, restriction, and interactive bond mechanism and intelligent multi-factor balancing algorithm were also studied. Finally, the integration of the collaborative optimization distribution scheme and strategy for food production, energy, and water resource utilization in the Yellow River basin was demonstrated. Results show that, by collaborative optimization and comprehensive allocation of water resources, energy, and food, the average annual water supply is expected to be 53.560 billion m³, increased by 2.398 billion m³. Both the food production distribution and energy production structure and scale are to be optimized; with an increase of 12%, per capita yield of food will reach 416 kg. Coal mining, oil mining, and total thermal power installed capacity will increase by 2.86 times, 4.08 times, and 0.80 times, respectively. According to the results, a guaranteed degree of water resources for energy development and food production security can be significantly improved, with domestic and ecological water demand given the highest priority in the model. Meanwhile, increased food and energy production can be realized, as well.