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Regional land use transitions driven by the adaptive reconciliation of existing land use conflict with socioeconomic development can lead to positive economic effects as well as new land use conflict. Although research on land use transition has progressed considerably, limited studies have explored the spatiotemporal dynamic pattern of land use conflict during the land use transition period. Previous evaluation approaches on land use conflict that mainly focus on status or potential conflict lack conflict intensity evaluation during the land use transition process. A new spatially explicit evaluation framework of land use conflict that directly examines three aspects of conflict, namely, ecological and agricultural (EAC), agricultural and construction (ACC), and ecological and construction (ECC) land conflicts based on ecological quality and agricultural suitability, is proposed in this study. The spatiotemporal dynamic pattern and driving factors of land use conflict in the Yangtze River Economic Belt of China in the period of 2000–2018 are evaluated. The results indicated that comprehensive land use conflict (CLUC) intensity slightly decreased by 9.91% and its barycenter showed a trend toward the west during 2000–2018. ACC is the most drastic conflict among the three aspects of conflict. The mean intensity of ACC reduced remarkably by 38.26%, while EAC increased by 33.15% and ECC increased by 28.28% during the research periods. The barycenter of EAC moved toward the east while the barycenter of ACC and ECC moved toward the west. The changes in the intensity and spreading pattern of land use conflict indices demonstrated the changes in the pattern of territorial space development. Total population, population density, per capita GDP, number of mobile phone users, and road density were strong drivers that influenced the land use conflict of territorial space. Multiple policy recommendations including improving territorial space planning and governance ability, and improving land use efficiency, were proposed to manage and resolve the land use conflict of territorial space. The results and conclusions of this study will help improve future regional land use policies and reduce land use conflict.