Alterations in plant litter inputs into the soil are expected to significantly affect soil greenhouse gas (GHG) emissions. However, the influence on boreal forest soils is not clear, given the large amount of accumulated soil organic matter that may buffer the impacts from the input of fresh litter. In this study, we conducted a litter manipulation experiment to explore the effects of the litter layer on soil GHG fluxes in a Dahurian larch (Larix gmelinii) forest ecosystem in northeastern China. Three litter treatments were implemented, namely aboveground litter removal (LR), litter double (LD), and unchanged litter input (CK). The associated microclimate, litter characteristics, and soil properties were also measured. The results showed that this larch forest soil acts as a source of CO2 and N2O but acts as a sink for CH4 for all litter manipulation treatments. LD increased the soil CO2 and N2O fluxes by 15% and 34%, while LR decreased them by 8% and 21%, respectively. However, soil CH4 uptake decreased by 34% in LD treatment and increased by 22% in LR treatment, respectively. Litter manipulation treatments can not only affect soil GHG fluxes directly but also, via their effects on soil MBC, NH4+−N, and NO3−−N content, indirectly affect variations in soil CO2, CH4 and N2O fluxes, respectively. Our study highlights the importance of the plant litter layer in regulating soil GHG between the atmosphere and soil in a Dahurian larch forest ecosystem, especially for litter addition. Considering the natural increase in litter quantity over time, this important regulatory function is essential for an accurate estimation of the role of boreal forests in mitigating future climate change.