Optimizing land use structure in urban agglomerations is essential to mitigating climate change and achieving carbon neutrality. However, the studies on low-carbon (LC) land use in the urban agglomeration based on carbon neutrality are still limited and lack the consideration of the optimized land ecological benefits. To reduce land use carbon emissions (LUCEs) and improve the ecological benefits of urban agglomerations, we constructed the framework of land use structure optimization (LUSO) under carbon neutrality. Then, in view of land use quantity structure and spatial distribution, we compared the results of LUCEs and the ecological benefits of the Chengdu-Chongqing urban agglomeration (the CCUA) in 2030 under different scenarios. The results showed that in 2030, the LUCEs of the CCUA is 3481.6632 x 10(4) t under the carbon neutral scenario (CN_Scenario), which is significantly lower than the baseline scenario (BL_Scenario) and 2020. In the CN_Scenario, the land use/cover change (LUCC) in the CCUA is more moderate, the aggregation degree of the forestland (FL), grassland (GL), wetland (WL), and water (WTR) patch area deepens, and the overall landscape spreading degree is increased, which is more conducive to play the ecological benefit of carbon sink land. The results can provide a reference for the more efficient use of land resource areas and the formulation of land use and spatial planning.