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In the context of ensuring national food security, high-intensity agricultural production and construction activities have aggravated the conflicts between agricultural and ecological spaces in ecologically fragile areas, which have become one of the most important factors hindering regional sustainable development. This study took Lin’an District, a typical hilly region of southeastern China, as an example. By constructing a landscape ecological risk evaluation model, land-use conflicts between agricultural and ecological spaces were identified, spatial autocorrelation and topographic gradient characteristics were analyzed, and land-use conflict trade-off mechanisms were proposed. During 2008 and 2018, the degree of land-use conflict in Lin’an District displayed an increasing trend, and the proportion of severe conflicts increased obviously. Slope is the main factor affecting land-use conflicts in a hilly region and shows a negative correlation, mainly because areas with flat terrain are more conducive to human activities. Based on the characteristics of land-use conflicts in Lin’an District, conflict trade-off mechanisms were proposed to provide a theoretical basis and practical support for land-use conflict management. Our study provides scientific evidence for sustainable land-use planning and ecological management in ecologically fragile areas.