In addition to expanding agricultural land area and intensifying crop yields, increasing the global trade of agricultural products is one mechanism that humanity has adopted to meet the nutritional demands of a growing population. However, climate change will affect the distribution of agricultural production and, therefore, food supply and global markets. Here we quantify the structural changes in the global agricultural trade network under the two contrasting greenhouse gas emissions scenarios by coupling seven Global Gridded Crop Models and five Earth System Models to a global dynamic economic model. Our results suggest that global trade patterns of agricultural commodities may be significantly different from today's reality with or without carbon mitigation. More specifically, the agricultural trade network becomes more centralised under the high CO2 emissions scenario, with a few regions dominating the markets. Under the carbon mitigation scenario, the trade network is more distributed and more regions are involved as either importers or exporters. Theoretically, the more distributed the structure of a network, the less vulnerable the system is to climatic or institutional shocks. Mitigating CO2 emissions has the co-benefit of creating a more stable agricultural trade system that may be better able to reduce food insecurity.