Permafrost peatlands, as large soil carbon pools, are sensitive to global warming. However, the effects of temperature, moisture, and their interactions on carbon emissions in the permafrost peatlands remain unclear, when considering the availability of soil matrixes. The permafrost peatland (0–50 cm soil) in the Great Xing'an Mountains was selected to explore the deficiency. The cumulative carbon dioxide (CO₂) and methane (CH₄) emissions from soil were measured under different temperatures (5 °C, 10 °C, and 15 °C) and moisture content (130%, 100%, and 70%) treatments by the indoor incubation. The results showed that the soil carbon and nitrogen matrix determined soil carbon emissions. Warming affected the availability of soil carbon and nitrogen substrates, thus stimulating microbial activity and increasing soil carbon emissions. With soil temperature increasing by 10 °C, soil CO₂ and CH₄ emission rates increased by 5.1–9.4 and 3.8–6.4 times respectively. Warming promoted soil carbon emissions, and the decrease of moisture content promoted CO₂ emissions but inhibited CH₄ emissions in the permafrost peatland. Soil moisture and the carbon and nitrogen matrix determined the intensity of CO₂ and CH₄ emissions. The results were important to assess soil carbon emissions from permafrost peatlands under the impact of future climate warming and to formulate carbon emission reduction policies.