In this study, the variation of greenhouse gas (particularly, carbon dioxide (CO₂) and methane (CH₄)) emissions and key factors influencing emission within the depth profile of two typical ombrotrophic bogs (BBM and SBM) were investigated by the Fourier Transform Infrared Spectroscopy (FTIR) technique and isotopic signature (δ¹³C and δ¹⁴N). The results showed that (1) CO₂ concentration was decreasing with the depth in BBM where value mostly fluctuates at 3000 μmol/L, with a maximum value of 4210.74 μmol/L at 120 cm depth while CO₂ concentration of SBM increased first and then decreased with the depth. Moreover, CO₂ concentration of SBM fluctuated slightly above 60 cm, and fluctuated greatly below 60 cm, with a maximum value of 4191.94 μmol/L at 90 cm depth. Similarly, concentrations of CH₄ were increasing with depth in both sites and rapidly increased below 60 cm, the maximum values of CH₄ were 753.90 μmol/L at 260 cm depth and 543.51 μmol/L at 170 cm, respectively. (2) δ¹³C_CH4 of the investigated two sites had a low value, which demonstrated that a large amount of ¹²CH₄ was stored and behaves like carbon sink. Thereafter, value of δ¹³C_CO2 and the fractionation factor α_{c w} ere increasing with the depth in the two sites, which revealed that acetate fermentation might serve as a key methanogenic pathway of shallow layer, while CO₂ reduction was dominant in deeper layer. (3) The investigated results of C/N ratios, stable isotope, and FTIR indicating a low degree of organic matter decomposition, which may be due to the low dissolved organic carbon and pH values restrained the peat decomposition. This study provides scientific data supporting where contribution of northern peatland as an important carbon sink and further helps in regional/global carbon budgeting.