China and Russia are major agricultural countries with abundant agricultural resources, holding important global agricultural trade market positions. While the scale of China-Russia agricultural trade has maintained rapid growth, the embodied carbon emissions from agricultural products have also increased. This article first uses input-output data to construct a multi-regional input-output model under a total trade accounting method to calculate the carbon emission coefficients, trade value-added, and embodied carbon emissions of three categories of agricultural products traded between China and Russia from 2009 to 2019. Our results show that, from an industry perspective, Category C3 agricultural products have the highest carbon emission coefficients; Category C1 agricultural products have the highest export value-added. From the standpoint of imports and exports, Russia’s export value-added to China has proliferated in recent years and is slightly higher than that of Chinese exports to Russia; the embodied carbon emissions from Chinese agricultural products are higher than those from Chinese exports to Russia. We further examined the impact of trade scale, trade structure, and carbon emission intensity on embodied carbon, finding that these three factors have heterogeneous effects on the embodied carbon of agricultural trade for different industries and countries.