Climate change, driven by excessive greenhouse gas (GHG) emissions from agricultural land, poses a serious threat to ecological security. It is now understood that significant differences exist in the responses of soil GHG emissions and soil carbon (C) sequestration to the application of different C-based materials (i.e., straw, organic manure (OM), and biochar). Therefore, elucidating the mechanisms by which differences in the properties of these materials affect soil GHG emissions is essential to comprehensively investigate the mechanisms through which variations in material properties influence soil GHG emissions. Herein, we conducted a field experiment to evaluate the responses of soil GHG emissions to cropland application of different C-based materials and employed molecular modeling calculations to explore the mechanisms by which differences in the properties of these materials affect soil GHG emissions. The results showed that biochar demonstrated superior resistance to biochemical decomposition and soil GHG adsorption capacity, leading to a significant reduction in soil GHG emissions due to its excellent physicochemical properties. The active surface properties of straw and OM enhanced their interaction with decomposing enzymes and accelerated their biochemical decomposition. Wheatmaize rotation with biochar application reduced CO2 emissions by 1089.8 kg CO2eq ha(-1) and increased soil organic carbon by 141.8% compared to the control after one year. Collectively, these results contribute to the optimization of cropland application strategies for crop residues to balance soil C sequestration and soil GHG emissions, and to ensure sustainable agriculture and ecological security.