Abstract: Agricultural production is not only a major water user in the Yellow River Basin but also a major contributor to carbon emission. The comprehensive assessment and flow analysis of agricultural water-carbon footprints at the urban agglomeration level in the Yellow River Basin can facilitate synergistic management of water conservation and carbon reduction among these agglomerations, ultimately driving the basin towards high-quality development. Based on the constructed city-scale multiregional input-output (MRIO) model, we comprehensively assessed the water footprint and carbon footprint of agriculture in 71 cities in five national city clusters in the basin from the production and consumption perspectives. The flow of virtual water and embodied carbon between and within city clusters was also analyzed. The results showed that: (1) From a production perspective, the total agricultural water and carbon footprints were 33.62 billion m³ and 117.7 Mt, respectively, of which the city clusters of the Central Plains and the Shandong Peninsula were particularly prominent, accounting for 55.5% and 66.7%, respectively. The consumption perspective revealed a considerably lower impact, with a total of 12.47 billion m³ and 53.0 Mt, respectively. (2) The spatial distribution patterns of agricultural water-carbon footprints were similar, with some cities in the north and east having higher water-carbon footprints, while cities in the south and west had relatively lower ones. Cities in the east and south had lower water-carbon footprint intensities, while cities in the north and west had relatively higher intensities. (3) Agricultural virtual water and embodied carbon mainly flowed within city clusters, accounting for 78.7% and 80.5% of the total inter-city transfers, respectively, and were mainly concentrated in the city clusters of Central Plains and the Shandong Peninsula. Cities that exported virtual resources were typically characterized by agricultural production and processing, while those importing virtual resources were predominantly regional consumption and economic hubs. It was recommended to formulate and improve agricultural water-saving and carbon-reduction measures based on the characteristics of urban agglomerations, strengthen collaborative cooperation and resource sharing among urban agglomerations, and jointly promote the green transformation and sustainable development of agriculture in the Yellow River Basin.