Excessive greenhouse gas (GHG) emissions from cropland pose a significant threat to ecological security. Recently, crop residues have emerged as promising strategies for enhancing soil carbon (C) sequestration and have been widely applied in various forms (e.g., biochar, straw, and organic manure) in fields, demonstrating differential effects on soil GHG emissions. The diverse crop residue utilizations can potentially modulate their molecular-scale surface properties, however, the mechanisms of these changes influencing soil C-containing GHG emissions remain unclear. To address this knowledge gap, we conducted field monitoring to assess the response of soil C-containing GHG emissions to the application of different organic materials (biochar, straw, and organic manure). Concurrently, density functional theory calculations were employed to explore the influence of their surface physicochemical properties on soil C-containing GHG emissions. Our results indicated that biochar's superior physicochemical properties, including its aromatic C-stabilized structure and favorable electron configuration, contributed to its enhanced resistance to biochemical decomposition, as well as its superior adsorption capacity for soil C-containing GHGs. Consequently, biochar application resulted in a net emission reduction of 435.51 kg CO(2)eq ha(-) (1) compared to NPK, primarily through reduced CH4 emissions in the wheat-corn rotation. In contrast, the rapid biochemical decomposition of straw, while leading to a 15.25 % increase in soil organic carbon, resulted in a net emission increment of 2616.52 kg CO(2)eq ha(-1) compared to NPK. These findings provide valuable insights for optimizing field application strategies of crop residues to balance soil C sequestration and GHG emissions, ultimately promoting sustainable agriculture and addressing climate change.