Wetlands are hot spots for particulate organic matter (POM) supply into rivers, which link the land‐ocean transfer in the global carbon cycle. However, the source, composition, and seasonal variability of POM carried by wetland‐draining rivers are poorly constrained. Here we combine bulk and source‐specific biomarker analyses to investigate the fluvial POM biogeochemistry of the Black and White Rivers draining from the Zoige wetland. We find that POM was dominated by terrestrial organic matter including high‐molecular‐weight (HMW) lipids, branched glycerol dialkyl glycerol tetraethers, and lignin phenols. However, fluvial POM was rich in HMW lipids and poor in lignin phenols compared to the catchment soils, possibly due to hydrodynamic sorting and dissolution processes. While lignin phenol concentrations were higher in the wet season, HMW lipid concentrations were lower. Additionally, lignin phenols increased with total suspended solids, while HMW lipids decrease. These contrasts imply an enhanced input of lignin‐rich particles from soil surface layers in the wet season, diluting HMW lipids. Compared with that in other rivers around the world with a higher forest coverage in the catchment, POM in the Black and White Rivers draining grass‐dominated wetlands had a much higher ratio of HMW fatty acids to lignin phenols. Our results represent a benchmark study highlighting compositional characteristics of fluvial POM exported from the Zoige wetland and the divergent behavior of molecular components during fluvial transfer. Such information is vital for assessing future changes in the Zoige wetland, given its high vulnerability to climatic and land use changes.