Peatlands in permafrost region are large carbon pools sensitive to global warming. However, the effects of increased temperature on carbon emissions and associated microbial abundances of peatlands under anaerobic condition remain largely unknown, especially when considering depths. For supplementing the deficiency about this, we collected soil from 0 to 150 cm depth of a permafrost peatland in the Great Hing'an Mountain and incubated at 5 and 15 °C for 55 days under anaerobic condition. Soil CO2 and CH4 emissions were detected during incubation, and inorganic nitrogen, dissolved organic carbon, and carbon-cycling microbial abundances were analyzed at the end of incubation. Results showed that emission rates and cumulative emissions amount of CO2 and CH4 at 15 °C across all soil depths were higher than those observed at 5 °C. Specifically, 0–20 cm and 20–40 cm layers had the highest CO2 emission rates and cumulative emission amounts, whereas the 40–60 cm and 60–80 cm layers had the highest CH4 emission rates and cumulative emission amounts. Mean temperature sensitivity (Q10) values of CO2 and CH4 were 2.39 and 55.49 respectively. Q10 values of bacteria, fungi, archaea, methanogen, and methanotroph abundances were 1.17, 3.85, 1.75, 1.68, and 1.66 respectively, which were calculated by the abundance ratio of microbial functional gene at 15 °C and 5 °C. Similar to the trend of CO2 emissions, high bacteria, fungi, archaea, methanogen, and methanotroph functional gene abundances were also observed in 0–20 cm and 20–40 cm layers, and such abundances increased along with temperature increasing. In sum, elevated temperature enhances the carbon emission of peatland in permafrost region, and the warming simulated CO2 emission is linked to the abundances of carbon-cycling microorganisms. •Soil CO2 and CH4 emissions at 15 °C are higher than at 5 °C across all soil depths.•Active layer soil has the highest CO2 emission amounts in permafrost peatland.•CH4 emissions are highest in the transition layer and its adjacent active layer.•Warming stimulated CO2 emission is linked to C-cycling related microbial abundance.