This study addresses the escalating environmental challenges linked to global climate change by focusing on carbon emissions in the agricultural sector, which notably contributes about one-third of total global greenhouse gas emissions. Utilizing five provinces in Southwest China as case studies, this research constructs an evaluation index system to assess agricultural carbon emissions, ecological environment, and agricultural economy from 2012 to 2021. Through the entropy value method, the coupling coordination model, and the obstacle degree model, the study evaluates the integration and coordination among these three dimensions and identifies the primary obstacles to their development. The findings indicate a generally unified direction of improvement in the coupling and coordination between agricultural carbon emissions, ecological conditions, and rural economy, reflecting significant progress in regional sustainable development. Key challenges identified include urban population density, waste management, sewage treatment capacity, agricultural output, and rural per capita disposable income. The study provides targeted recommendations for advancing eco-agriculture and achieving low-carbon production, promoting a comprehensive approach to addressing these challenges.