Abstract: Integrating ecosystem services into the evaluation of territorial space utilization efficiency and land use decision-making is crucial for promoting the sustainable management of regional territorial space. This study develops an evaluation index system for the utilization efficiency of agricultural, urban, and ecological land spaces, incorporating different types of ecosystem services. Using the SBM-Undesirable model, spatial autocorrelation analysis, and spatial econometric models, and taking the Yellow River Basin as a case study, this research analyzes the utilization efficiency of different territorial spaces under ecosystem service-oriented management, as well as their coupling coordination degree and influencing factors. It identifies areas needing improvement and proposes policy recommendations. The research shows that: 1) There are significant spatiotemporal differences in the utilization efficiency of the three types of territorial space in the Yellow River Basin. Urban land space utilization efficiency remains extremely low, with values below 0.2. Ecological land space utilization efficiency remains stable at a medium level. Agricultural land space utilization efficiency is relatively high and increased from 0.38 in 2000 (low level) to 0.62 in 2020 (high level) during the study period. 2) The comprehensive efficiency and coupling coordination degree of territorial space utilization in the Yellow River Basin are low but generally coordinated. Although some improvement occurred from 2000 to 2020, over 70% of county-level efficiency composite values remained below 0.4 in 2020, and more than 20% of counties exhibited imbalances in the utilization efficiency of the three land space types. The downstream region has the highest comprehensive efficiency and coupling coordination degree, maintaining a generally coordinated state. From 2000 to 2020, the proportion of counties with severe and mild imbalances consistently declined. As agricultural spatial efficiency improved in the middle and lower reaches, areas with extremely low comprehensive efficiency and imbalances in the three types of territorial space utilization significantly decreased. The upstream region has generally lower comprehensive efficiency and coupling coordination degrees than the middle and lower reaches, indicating significant potential for improving the utilization efficiency of ecological and urban spaces. 3) From 2000 to 2020, the areas requiring improvement in agricultural and ecological land utilization efficiency in the basin gradually decreased, while those with improved urban spatial utilization efficiency first expanded and then declined. Moreover, human activities and land use have a greater impact on territorial space utilization efficiency than natural conditions. Significant differences exist in efficiency improvements and influencing factors among the upper, middle, and lower reaches. The middle and upper reaches have a broad and diverse range of efficiency improvement areas, with the upper reaches primarily focusing on ecological land utilization efficiency. Ningxia remains a key area for improving ecological land utilization efficiency, while the middle reaches mainly focus on agricultural and urban spatial efficiency improvements. The range of efficiency improvement areas in the lower reaches is significantly smaller, primarily focusing on ecological and urban spatial utilization efficiency improvements. Based on the analysis of influencing factors across the upper, middle, and lower reaches, developing territorial space management strategies that balance utilization efficiency and ecosystem services can support high-quality development in the Yellow River Basin and national ecological civilization construction.