Abstract: Spatial development is ever prominent in the middle and upper reaches of the Yellow River in recent years, due mainly to the fragile ecological environment. This article aims to explore the optimization and allocation of land use structure and layout for ecological protection and high-quality development in the Yellow River Basin. The middle and upper reaches of the Yellow River were taken as the research object. The land use, socio-economic, and natural environment datasets were collected from 2010 and 2020. A composite optimization was carried out on the land use structure and layout using multi-objective programming (MOP) and PLUS models. Firstly, a multi-objective model was constructed with three scenarios as objective functions: ecological protection scenario (economic benefit to ecological benefit target ratio of 1:4), economic development priority scenario (economic benefit to ecological benefit target ratio of 4:1), and economic ecological balanced development scenario (economic benefit to ecological benefit target ratio of 1:1). The total land area, cultivated land ownership, and ecological environment protection were used as the constraints, in order to obtain land use structure data under these three scenarios; Secondly, plugin Markov Chain of the PLUS model was utilized to predict the land use structure data for 2030 under the inertial development scenario; Finally, 15 driving factors were selected, including population, vegetation index (NDVI), GDP, distance to railways, distance to highways, distance to main roads, distance to secondary roads, distance to city center, soil type, distance to rivers, annual average temperature, annual average rainfall, DEM, slope, and aspect. High sensitivity areas under national nature reserves and ecological priority scenarios were set as the limiting conversion conditions. The PLUS model was used to spatially position the future land use patterns, and then adjust the trends in the study area under four scenarios. The optimal configuration scheme of regional land use structure and layout was proposed to balance the ecological protection and economic development. The results indicate that: 1) There were significant differences in the proportion structure of land use among the four development scenarios; 2) There was a more reasonable configuration of regional land use structure and spatial layout under the ecological economic equilibrium scenario, compared with the rest scenarios. The overall equilibrium scenario was superior to the rest from the perspectives of land use proportion structure, spatial pattern, and overall benefits. The comprehensive benefit value was 1 948.100 billion yuan, and the economic benefit (1 222.388 billion yuan) increased by 4.07%, compared with the ecological protection scenario. The ecological value (725.712 billion yuan) also increased by 2.32%, compared with the economic priority scenario; 3) The comprehensive benefit value was 2 027.396 billion yuan under the scenario of prioritizing economic development, indicating the highest among the four. The finding can provide the theoretical basis and decision-making to optimize the land use structure and pattern prediction in the middle and upper reaches of the Yellow River.