The addition of litter may induce greenhouse gas (GHG) emissions to varying degrees depending on the mineral soil and the organic horizon. An assessment was made to deduce the impact of different litter addition rates on soil GHG emissions, physicochemical properties, and the abundance of functional genes involved in carbon and nitrogen cycles in both the organic horizon and mineral soil. Compared with soil without litter amendment, cumulative CO2 emissions increased by 6.85% to 11.87% in organic soil and by 16.66% to 54.43% in mineral soil. However, there was no significant difference in cumulative N2O emissions in the organic soil layers. Cumulative N2O emissions increased by 26.03% to 172.63% in the mineral soil. Soil dissolved organic carbon (DOC) increased by 21.63% to 40.87%, while NO3− decreased by 22.03% to 57.24% with litter input. Furthermore, soil pH and dissolved organic nitrogen decreased by 1.34% to 3.19% and 13.28% to 21.51%, respectively, whereas NH4+ increased by 40.28% to 81.04% in the mineral soil compared with with soil without litter addition. Following litter amendments, changes in N2O emissions were mainly driven by variations in soil physicochemical properties in the mineral soil, whereas in the organic horizon soil, they were influenced by the amoA2 gene. In the organic horizon soil, both labile (xylA, a xylose isomerase-related gene) and recalcitrant (chiA, an endochitinase-related gene) carbon degradation genes, along with DOC, played a dominant role in soil CO2 emissions. The recalcitrant carbon degradation related gene (lig, a lignin degradation related gene), along with DOC and pH, contributed to CO2 emissions in the mineral soil. This study enhances our understanding of how GHG emissions respond to litter accumulation in the organic horizon and mineral soil and highlights the importance of litter management in mitigating GHG emissions in agricultural environments.