Abstract: Food security and global climate change are widely recognized as two of the most formidable challenges confronting human society. In the context of efforts to mitigate climate warming while ensuring food security, agricultural soils are under dual pressures to both improve carbon sequestration and increase productivity. Deep soils (> 30 cm) represent a crucial component of the soil carbon cycle in terrestrial ecosystems, with more than half of the soil organic carbon stock in these deep soils. Understanding the mechanisms underlying organic carbon sequestration in deep agricultural soils, as well as exploring effective regulatory strategies, is of paramount importance for addressing both climate change and food security concerns. Given progress has been made in understanding the turnover of topsoil organic carbon, the dynamics of deep soil organic carbon remain insufficiently explored. This review provides a comprehensive overview of the sources and stability mechanisms of deep soil organic carbon, focusing on the methods of carbon sequestration in deep soil layers in agroecosystem. Finally, the review identifies key future research directions in deep soil carbon sequestration, aiming to contribute valuable insights for advancing research on soil carbon management in agroecosystems.