Coastal wetlands are active transitional ecotones between land and ocean, and are considered as hot spots of organic matter processing within the global carbon cycle, which dissolved organic matter (DOM) plays a critical role. In this study, combined use of ultrahigh-resolution mass spectrometry (FT-ICR MS) and complementary optical techniques was conducted to assess the detailed molecular composition of DOM in the temperate Liaohe coastal wetland (LCW), NE China in respect to the differences in DOM composition from surface water to sediment pore water. Significant positive correlations between salinity and dissolved organic carbon (DOC) concentrations were observed in both surface waters and pore waters. Pore water DOM is generally characterized by lower protein-like fluorescence and biological index, but higher humification and humic-like fluorescent components than those in surface water DOM. Corresponding to the optical properties, FT-ICR MS measurements show that pore water DOM has higher proportions of heteroatoms, aromaticity index, O/C ratios, unsaturated aliphatics, and peptides, but lower average H/C ratios compared to surface water DOM across locations with different marsh plant species (rice (Oryza sativa), reed (Phragmites australis), Seablite (Suaeda Salsa)) and salinity (0.5 to 51.5 psu). The results suggest that selective preservation for polyphenols, lignin degradation intermediates (highly unsaturated compounds), and microbial resynthesis of heteroatomic compounds are involved in the processing of DOM from surface water to pore water, leading to the formation of higher molecular weight and sulfur-containing molecules. The abundant CHOS compounds could be related to the early diagenetic sulfurization of DOM in sediments. Our unique data set should provide new clues for a comprehensive understanding of the molecular dynamics of DOM in coastal wetlands.