<p>To support the dual goals of carbon neutrality and peak carbon, along with the regional coordinated development strategy, this paper analyzes the spatio-temporal dynamics of carbon sequestration, carbon emissions, and carbon offset effect at the county scale in the Central Yunnan Urban Agglomeration. A carbon management evaluation system was also established. Integrated zoning for carbon compensation and management was conducted based on the carbon offset effect, the economic-social-ecological composite index, and the coupling coordination degree of each county. Over the past two decades, both carbon sequestration and carbon emissions have shown an upward trend in the Central Yunnan Urban Agglomeration. Although the total carbon sequestration can offset the overall carbon emissions, analysis at the county level reveals significant spatial disparities in the carbon offset effect. A multi-core structure was observed, exhibiting a spatial pattern of "low in the center and high at the periphery." Based on the carbon offset effect and local economic, social, and ecological conditions, the Central Yunnan Urban Agglomeration was categorized into six zones, and differentiated management strategies were proposed for each. This study and its zoning scheme are crucial for clarifying regional carbon responsibilities and for developing and implementing tailored carbon strategies and planning.</p>