The change in land use leads to territorial spatial conflict. Territorial spatial conflicts mainly show that the boundaries of agricultural space, urban space, and ecological space overlap each other and interfere with each other’s functions, which will have a negative impact on regional high-quality development. The Aksu River, the most principal source of the Tarim River, the largest instream river in China, is a key area for maintaining ecological security in Northwestern China. It is highly significant to identify the spatial conflict characteristics of land use in this region to promote the sustainable use of regional land resources, optimization of spatial patterns, and the balance between economic construction and ecological environmental protection in mountainous areas. This paper takes the Aksu River Basin as the research area. Using Arcgis 10.8 software, Yaahp software, and SPSSAU software, it builds a land use spatial conflict measurement model based on a quantitative analysis of land use changes from 1990 to 2020 and explores the spatial and temporal evolution characteristics of land use conflicts in the Aksu River Basin. The results show that: (1) From 1990 to 2020, the spatial conflict pattern of the study area was dominated by ecological spatial conflicts. The spatial conflict area shows dynamic changes, but the overall trend is decreasing. (2) The spatial conflict pattern of territorial space in the Aksu River Basin has basically formed, and the three types of spatial conflicts are closely related to the level of local economic development. (3) Ecological spatial conflicts are mainly distributed in high-altitude mountains, river valleys, and oasis-to-desert transition areas. Urban spatial conflicts are mainly distributed in the middle and lower reaches of the Aksu River plain oasis. Agricultural spatial conflicts are scattered but large in scale, with small differences in the proportion of conflict distribution among the counties.

To achieve high-quality sustainable development in arid areas based on the concept of ecological civilization, it is necessary to deeply study the territorial spatial structure characteristics. Taking the Aksu River Basin, an important ecological security barrier in northwest China, as an example, this paper follows the research idea of “feature analysis-suitability evaluation-conflict identification analysis-optimization” and constructs a comprehensive model based on the AHP-entropy weight comprehensive evaluation method, ArcGIS spatial identification analysis, variance coefficient-TOPSIS method, and NRCA. A comprehensive model based on the AHP-entropy power integrated evaluation method, ArcGIS spatial identification analysis, variance coefficient-TOPSIS method, and NRCA was constructed to guide the optimization of the territorial spatial layout by exploring the characteristics of territorial spatial pattern, the suitability of territorial spatial development, the identification of territorial spatial conflicts, and the efficiency and functional advantage of territorial spatial utilization in the study area. The results show that: (1) The spatial type of territorial space in the Aksu River Basin from 2000 to 2020 is dominated by ecological space, agricultural space, and urban space, and the three spatial boundaries are irregularly interlaced. (2) The spatial utilization conflict pattern of the Aksu River Basin has formed, and the general conflict area is overgrowing. (3) The overall efficiency of territorial utilization in the Aksu River Basin is low, with significant differences among county administrative units. (4) After optimization, the three types of space in the watershed are adjusted and refined into six functional areas: basic farmland protection area, rural development area, ecological protection red line area, ecological control area, urban development area, and industrial supporting construction area.