Water-land-carbon nexus is one of the hotspots in resources and environment research in recent years. Studies on the flow tracks of agricultural water, land, carbon footprints can reveal the cross-regional environmental influences bring about by agricultural production and trade, which is of great significance for the optimal allocation and sustainable management of water and land resources and the collaborative carbon emission reduction in different regions. Taking the 30 provincial administrative regions of China as the study cases, this paper calculates the agricultural water, land and carbon footprintss by multi-regional input-output analysis, and scientifically explores and identifies the spatial patterns, flow tracks and correlation characteristics of the agricultural water, land and carbon footprints. The main conclusions are as follows:(1) The spatial patterns of the agricultural water, land and carbon footprint at the provincial scale in China are quite different, which can be attributed to the diversity of natural conditions, social economy, industrial structure, methods of cultivation and planting formation in different regions. (2) From the perspective of the inter-provincial flow tracks, the agricultural water, land and carbon footprints roughly transfer from the western and the northern regions to the eastern and the southeastern regions of China, which is closely related to the supply and demand of agricultural products market. This indicates that the consumption of agricultural products in the eastern and the southeastern regions has led to the virtual occupation of water and land resources and hidden carbon emissions in the western and the northern regions. (3) There are correlations among the agricultural water, land and carbon footprints and the intensities, but the status and degree of correlations vary in different regions. Economic development, regional industrial structure, natural conditions and other factors can affect the consumption intensity of water, land and carbon, which will further affect the correlation between the them. The flow tracks of agricultural water, land, carbon footprints show significant spatial correlation characteristics. The spatial correlation network is unbalanced, and the correlation channels need to be enriched. (4) It is suggested that the agricultural technology innovation in the future should be strengthened, and the level of mechanization utilization and intelligent production should be improved. Large-scale land management should be promoted to realize the economical and intensive utilization of water and land resources. The agricultural ecological compensation measures based on the cross-regional impacts of water-land-carbon nexus should be adopted to realize the cooperation of provinces for the carbon emission reduction and resource optimization in China.