Abstract: Ecosystem services can often be integrated to evaluate the utilization efficiency of territorial space and land use decision-making in the sustainable management of regional natural sources. In this study, an evaluation index system was developed for the utilization efficiency of agricultural, urban, and ecological land spaces. Different types of ecosystem services were also incorporated using the SBM-Undesirable model, spatial autocorrelation analysis, and spatial econometric models. A case study was taken in the Yellow River Basin from 2000 to 2020. A systematic analysis was made on the utilization efficiency of different territorial spaces under ecosystem service-oriented management, as well as their coupling coordination degree and influencing factors. Finally, some recommendations were proposed to identify the areas needed. The results show that: 1) There were significant spatiotemporal differences in the utilization efficiency of the three types of territorial space in the Yellow River Basin. The extremely low efficiency in urban land space utilization remained with the values below 0.2. The utilization efficiency of ecological land space was stable at a medium level. The relatively high efficiency of agricultural land space utilization was achieved to increase from 0.38 in 2000 (low level) to 0.62 in 2020 (high level) during the study period. 2) There was a low comprehensive efficiency and coupling coordination degree of territorial space utilization, indicating generally coordinated patterns. Although some improvement occurred from 2000 to 2020, over 70% of county-level efficiency composite values remained below 0.4 in 2020. More than 20% of counties exhibited imbalances in the utilization efficiency of the three land space types. The downstream region shared the highest comprehensive efficiency and coupling coordination degree, indicating a generally coordinated state. There was a consistently declining proportion of counties with severe and mild imbalances. Agricultural spatial efficiency was improved in the middle and lower reaches. As such, there was a significant decrease in the areas with the extremely low comprehensive efficiency and imbalances in the three types of territorial space utilization. The upstream region showed generally lower comprehensive efficiency and coupling coordination degrees than the middle and lower reaches. Significant potential was found to improve the utilization efficiency of ecological and urban spaces. 3) There was a gradual decrease in the required areas in the agricultural and ecological land utilization efficiency in the basin. While the areas with the improved efficiency of urban spatial utilization first expanded and then declined in the study period. Moreover, human activities and land use share a greater impact on territorial space utilization efficiency than natural conditions. There were significant differences in the efficiency and influencing factors among the upper, middle, and lower reaches. The middle and upper reaches shared a broad and diverse range of efficiency improvement areas. Among them, the upper reaches were focused primarily on ecological land utilization efficiency. Specifically, Ningxia remained one of the most key areas to improve the utilization efficiency of ecological land. While the middle reaches were focused mainly on the agricultural and urban spatial efficiency. There was a relatively smaller range of efficiency improvement areas in the lower reaches, particularly on the efficiency of ecological and urban spatial utilization. The influencing factors were determined among the upper, middle, and lower reaches. Territorial space strategies were developed to balance the utilization efficiency and ecosystem services. The findings can provide a strong reference to support the high-quality development in the Yellow River Basin.