Natural wetlands are known to store huge amounts of organic carbon in their soils. Despite the importance of this storage, uncertainties remain about the molecular characteristics of soil organic matter (SOM), a key factor governing the stability of soil organic carbon (SOC). In this study, the molecular fingerprints of SOM in a typical freshwater wetland in Northeast China were investigated using pyrolysis gas-chromatography/mass-spectrometry technology (Py-GC/MS). Results indicated that the SOC, total nitrogen (TN), and total sulfur contents of the cores varied between 16.88% and 45.83%, 0.93% and 2.82%, and 1.09% and 3.79%, respectively. The bulk δ13C and δ15N varied over a range of 9.85‰, between -26.85‰ and -17.00‰, and between -0.126‰ and 1.002‰, respectively. A total of 134 different pyrolytic products were identified, and they were grouped into alkyl (including n-alkanes (C:0) and n-alkenes (C:1), aliphatics (Al), aromatics (Ar), lignin (Lg), nitrogen-containing compounds (Nc), polycyclic aromatic hydrocarbons (PAHs), phenols (Phs), polysaccharides (Ps), and sulfur-containing compounds (Sc). On average, Phs moieties accounted for roughly 24.11% peak areas of the total pyrolysis products, followed by Lg (19.27%), alkyl (18.96%), other aliphatics (12.39%), Nc compounds (8.08%), Ps (6.49%), aromatics (6.32%), Sc (3.26%), and PAHs (1.12%). Soil organic matter from wetlands had more Phs and Lg and less Nc moieties in pyrolytic products than soil organic matters from forests, lake sediments, pastures, and farmland. δ13C distribution patterns implied more C3 plant-derived soil organic matter, but the vegetation was in succession to C4 plant from C3 plant. Significant negative correlations between Lg or Ps proportions and C3 plant proportions were observed. Multiple linear analyses implied that the Ar and Al components had negative effects on SOC. Alkyl and Ar could facilitate ratios between SOC and total nitrogen (C/N), while Al plays the opposite role. Al was positively related to the ratio of dissolved organic carbon (DOC) to SOC. In summary, SOM of wetlands might characterize by more Phs and lignin and less Nc moieties in pyrolytic products. The use of Pyrolysis gas-chromatography/mass-spectrometry (Py-GC/MS) technology provided detailed information on the molecular characteristics of SOM from a typical freshwater wetland.