Objective Spatial conflict is a key bottleneck hindering the improvement of territorial spatial governance efficiency, which is particularly prominent in megacities with highly concentrated population and production factors. Scientifically identifying the intensity, driving factors, and evolutionary characteristics of territorial spatial conflicts can provide theoretical support and a practical basis for establishing a long-term governance system of territorial spatial conflicts. Methods Taking Chongqing as the study area, this study used land use data and natural-socio-economic data from 2000 to 2023. Following the analytical framework of “regional functional pattern evolution—conflict intensity identification—zoning-based optimized regulation and control”, it characterized the evolution of territorial spatial patterns, identified territorial spatial conflict intensity, and proposed zoning-based solutions for conflict regulation and optimization. Results (1) The overall territorial spatial pattern of the study area showed the evolutionary characteristics of “urban space expansion, agricultural space contraction, and marginal degradation of ecological space”. The intensity of evolution was closely related to economic development levels and topographic conditions: more intense in the relatively flat and economically developed main urban area, and relatively moderate in the northeastern and southeastern regions of Chongqing, which were economically less developed and had rugged terrain. (2) The overall level of territorial spatial conflict showed an increasing trend over time, forming a “core-periphery” diffusion pattern that highly overlapped with the direction of urban expansion. The level of conflict exhibited strong regional differentiation: conflict levels were high in the main urban area, extending from the central city to the urban fringe. In northeastern Chongqing, influenced by rugged terrain and population resettlement, conflict levels first decreased and then increased; while in southeastern Chongqing, conflict levels remained relatively low due to rugged terrain and lower economic development. (3) Zoning-based regulation strategies focusing on ecological restoration and governance, agricultural development and construction, and urban optimization were important pathways for mitigating or resolving territorial spatial conflicts. Conclusion From 2000 to 2023, territorial spatial conflict in the study area intensified overall, with significant regional differentiation in conflict levels. Zoning-based regulation strategies tailored to functional differentiation are a crucial approach to coordinating and resolving spatial conflicts.
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