Due to problems in the water resources allocation of Yellow River basin, the method of water consumption in proportional increase or decrease with the increasing or decreasing of river discharge may have negative effects on rational water utilization. Traditional scheduling methods could not coordinate the harmonious development between resources and society. In view of this, a multi-objective optimization model for water resource allocation was established in consideration of the impartiality and rationality of regional water use based on the actual situation of the Yellow River. Furthermore, the model was solved by applying improved genetic algorithm. Research results show that through the improved genetic algorithm, water resources of the mainstream Yellow River can be rationally and scientifically allocated to different segments. The rate of water scarcity in the whole study area is below 10% and the water allocation results meet the requirements of ecological flow of river cross-section, which also conform to the ecological and social requirements of development and utilization of water resources. The comprehensive benefits of water resources developed to the greatest extent.