The river-reservoir continuum drives a separation of sedimentation along the longitudinal hydrodynamic gradients, potentially causing imbalanced stoichiometric sedimentation. However, there are still uncertainties regarding the contribution of imbalanced stoichiometric sedimentation to methane emissions along this continuum. A 2-year field survey and in situ experiments were conducted in China's Three Gorges Reservoir (TGR), a river-valley-dammed reservoir. Sediments were trapped and collected to analyze for particulate carbon (C), nitrogen (N), and phosphorus (P) concentrations of different sizes in the summer flooded and winter dry seasons along the mainstem. Large amounts of sediments were deposited in the middle part of the TGR, particularly in the summer flood season. Hydrodynamic gradients structured imbalanced stoichiometric sedimentation patterns. Averaged particulate C:N:P proportions in the sediment layer along the upper, middle, and lower parts of the TGR in the first 30 years of reservoir operation were estimated to be 68:7:1, 97:8:1, and 151:13:1, respectively. The middle part of the TGR, being the "control point" of methane accumulation based on seasons, exhibited a shift in stoichiometry and stable isotope signatures, indicating that there was likely a shift in sources of POM. P, specifically in smaller size particles (<10 μm), seemed to be the potential key driver that regulates particulate C:N:P in the sediment of the TGR. Its sedimentation, primarily in the middle part of the TGR, contributed to the significant decreases in particulate C/P ratios and could possibly regulate long-term CH 4 accumulation in the reservoir.