The contradiction between urban expansion and ecological spatial protection is one of the urgent problems to be solved in the process of new urbanization and national territory spatial planning. As the core area for ecological protection and high-quality development in the Yellow River Basin, the Guanzhong Plain Urban Agglomeration is facing more severe ecological and resource stresses. However, relevant studies have mainly measured the ecological changes in the study area as a whole, and few studies have analyzed the multi-scale impacts of urban agglomeration development on ecological land, and neglected the urban fringe areas in urban agglomerations with the most drastic land changes and the most severe ecological stresses. Therefore, based on the land use data, combined with the land use transfer matrix, landscape index, and methods to estimate the area of ecological land indirectly affected by urban expansion, this article selects three scales (urban agglomerations, prefecture-level cities, and urban fringe areas) to analyze the direct and indirect impacts of urban expansion on ecological land from 1990 to 2018. The results show that:(1) the land use type of the urban agglomeration in the Guanzhong Plain is dominated by semi-ecological land (farmland), with an area accounting for more than 40%. The urban fringe areas are mainly semi-ecological land and built-up land. The proportion of built-up land in urban agglomerations increased from 3.67% in 1990 to 5.93% in 2018. The area of farmland decreased by 3,032.11 km², while the area of natural ecological land increased by 628.03 km². Affected by multiple policies such as the requisition-compensation balance of farmland and grain for green, the semi-ecological land and natural ecological land compensate for each other. (2) The direct impact of urban expansion on semi-ecological land is greater than that on natural ecological land, and the changes in land use transfer are similar at all scales, with the main source of new built-up land being farmland. The farmland in urban fringe areas is most prominently occupied by built-up land. (3) The indirect impact of urban expansion on the natural ecological land is greater than the direct impact and the indirect impact is different due to the different compensation mechanisms for farmland. Therefore, it is unreasonable to implement a unified farmland compensation policy for the urban agglomeration. It is necessary to consider the regional land resource and conditions and appropriately adjust the development and restraint policies, which is conducive to the sustainable development of the urban agglomeration.