Agriculture is a cornerstone of global sustainability, yet its water-energy-carbon (WEC) nexus interactions impose significant pressure on resource security and climate mitigation. China's agricultural sector, consuming 70 % of freshwater and contributing over 25 % of GHG emissions, faces urgent challenges in balancing productivity with environmental sustainability. Existing studies often overlook regional resource endowments and systemic synergies, necessitating an integrated assessment framework. This study proposed a tri-dimensional WEC nexus framework to evaluate agricultural sustainability across China’s provinces (2010–2020), incorporating regional water ecological and carbon stress index. It aimed to identify spatial heterogeneity, driving mechanisms, and optimization pathways for synergistic resource management. We integrated coupling coordination degree (CCD) models with geographically weighted regression (GWR) to quantify WEC system coordination and its drivers. Stress indices (SI) for water, energy, and carbon were derived from carrying capacity thresholds, addressing regional disparities in resource endowments and carbon sequestration potential. The results showed that only 10 % of Chinese provinces sustained a balanced WEC relationship, with imbalances which worsened over time. Provinces experiencing imbalances in 2010 faced further deterioration, posing a threat to agricultural sustainability. This trend was mainly attributed to unreasonable diesel usage and ratio of grain and cash crops. In addition, by synthesizing the results of GWR, we provided corresponding agricultural fund allocation policy recommendations for both national and provincial governments. The study advances WEC nexus theory by embedding regional carrying capacity into efficiency analysis. This framework offers a replicable tool for global agroecosystem sustainability assessments.