<p>The rapid expansion of global urbanization has amplified the complexity and fragility of regional land resource utilization, leading to frequent land use conflicts that hinder sustainable development. This study examines the spatial conflicts of land use (SCLU) in the Chengdu-Chongqing urban agglomeration through an ecological lens. A Spatial Composite Conflict Index (SCCI) was developed by integrating the Conflict Risk Index (CRI) and Ecological Value (EV) to quantify and analyze SCLU, while the Geo-detector model identified key driving factors. Moreover, the Potential Conflict Risk Index (PCRI) was developed by integrating the Patch-generating Land Use Simulation (PLUS) model with the Risk Matrix Approach (RMA), aiming to pinpoint areas with potential future conflict risks. Results indicate that from 2000 to 2020, SCLU in the Chengdu-Chongqing region decreased overall, with mild conflicts predominating. Conflict zones were primarily located on the urban periphery and dispersed within central areas, with intense conflicts concentrated in built-up zones. Key drivers of SCLU include GDP, population, temperature, and elevation, with human activities playing an increasingly prominent role. Predicted conflict risk warning zones for 2020–2030 encompass approximately 473.18 km², concentrated in the Chengdu-Deyang-Mianyang and Chongqing urban cores. The spatial pattern of conflict areas is expected to shift from scattered to more concentrated formations. This study underscores the importance of incorporating ecological perspectives into land use planning, offering valuable insights into the spatial–temporal dynamics of SCLU. The findings provide actionable policy recommendations for mitigating conflicts and fostering sustainable urban development in the Chengdu-Chongqing urban agglomeration.</p>