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Food security is an important foundation of national security, and the fundamental of guaranteeing national food security lies in arable land protection. In order to realize the protection of arable land in the context of ecological civilization, this paper designs a governance framework for arable land protection based on supply, empowerment, and control on the basis of the trinity of arable land protection policy of quantity, quality, and ecology, and constructs a multi-objective land use structure optimization model, and obtains a scenario prognosis for the optimal allocation of the land use structure by using a hybrid genetic algorithm. Taking County A as the specific research object, it can be seen by predicting the land use structure under the natural development scenario of County A that, relative to the status quo in 2023, the predicted share of arable land in 2050 has the largest decrease of 0.49%, and the shares of garden land, forest land, grassland and water area have all decreased, which is mainly converted into construction land (increased by 0.78%). From the Pareto frontier solution of land ecological benefit objective and economic benefit objective, three typical schemes of land use structure optimization were obtained, among which, the optimization scheme of balanced development of economy and ecology balanced economic and ecological development balanced economic development and ecological protection, and was selected as the optimization scheme of this paper. The increase of arable land area in this scheme is 0.38%, much higher than the -2.46% in the unoptimized case, which is in line with the requirement of arable land retention and can be used as a reference for further optimization of arable land protection framework.