Deciphering the role of soil organic matter on methylmercury production in wetlands is an important environmental topic in Tibet, where is the province with the largest number of international rivers, including the Yarlung Tsangbo River. In this study, total mercury (THg) and methylmercury (MeHg) contents in soils from wetlands along the YTR were detected, and roles of the molecular composition of soil organic carbon (SOC) in the formation of MeHg were explained in detail by pyrolysis-gas chromatography/mass spectrometry technology (Py-GC/MS). On average, THg and MeHg contents were 62.9 ng/g and 5.88 ng/g, respectively. About 12.6% of total Hg was in the form of MeHg. Unexpected high methylmercury levels occurred in wetland soils along the YTR. The topsoils (0-20 cm) had more THg but less MeHg contents than those in subsoils (20-48 cm). The proportion of MeHg to THg (RHg) was higher in subsoils than in topsoils independent of wetland types. Correlations between THg, MeHg, and SOC were weak in topsoils but strong in subsoils. Lignin and phenol moieties of SOC pyrolysis products were significantly and positively related to THg in topsoils, while positive or negative correlations were found between THg, MeHg, and pyrolysis products of SOC in subsoils at p < 0.05 level. C/N ratios were negatively related to RHg to a significant level in both topsoils and subsoils. Hg/C ratios correlated negatively with C/N ratios in both topsoils and subsoils at the 0.001-level, and larger coefficients in subsoils confirmed that older and high decomposed soil organic matter generally have high levels of Hg. Principle component analysis indicated that THg contents were closely related to plant-derived organic compounds, and MeHg contents were closely related to phytoplankton-derived organic compounds. Our findings suggested that molecular compositions of soil organic matter are critical to MeHg presentence in wetland soils along the YTR.