[Objective] The Jingjiang-Dongting Lake region, a critical river-lake system in the middle reaches of the Yangtze River, is crucial for flood mitigation, sediment regulation, and ecological conservation. This study aims to develop and apply an enhanced 2D water-sediment model incorporating a morphological acceleration factor (MF) to efficiently predict the bed deformation and sediment redistribution over a 30-year period, thereby providing a scientifically sound and computationally feasible tool for long-term morphodynamic prediction and sustainable management of large river-lake systems. [Methods] A 2D depth-averaged water-sediment model was established to solve shallow water equations and multi-fraction suspended sediment transport equations coupled with a bed deformation module. The governing equations were discretized using an unstructured finite volume method, with advection terms solved by the Euler-Lagrange method (ELM) to enhance numerical stability. To overcome the computational bottleneck of long-term simulations, the MF was introduced, linearly scaling the bed evolution per hydrodynamic time step to accelerate morphodynamic simulations while maintaining physical realism. The model domain covered the lower Jingjiang reach and the Dongting Lake and was discretized into unstructured cells with refined resolution along the main channel. Sediment was grouped into three size classes for suspended load and four for bed material, with gradation initialized from field surveys from 2003 to 2012. MF was determined at 7, 15, and 24 for sensitivity analysis. [Results] (1) The MF markedly improved computational performance. With MF values of 15 and 24, simulation time decreased to 42% and 30% of that for MF=7, corresponding to speed-up factors of 2.38 and 3.33, respectively. The spatially distributed erosion-deposition patterns remained consistent across different MF values, confirming the robustness of the approach. The total sediment deposition in Dongting Lake varied by less than 5% across scenarios, while the total erosion volume along the main stem exhibited higher sensitivity, with a maximum deviation of 9.1% between MF=24 and MF=7. These deviations were primarily localized and did not alter the long-term trends or magnitudes. (2) The mainstream of the Jingjiang River experienced sustained incision, with a total scour volume of 462 million m³ and an average bed incision of 1.86 m over 30 years. Local deposition occurred along convex banks due to curvature-induced secondary flows. Dongting Lake exhibited net deposition of 276 million m³, with an average siltation thickness of 0.09 m. Notably, the annual deposition rate in the lake decreased significantly over time—from 20 million m³ to about 6 million m³—representing an approximate 70% reduction and indicating a gradual approach toward a new morphodynamic equilibrium. Significant spatial variability in sediment redistribution was observed. The Jingjiang mainstream was dominated by scour, particularly in the deep channel, while point bars developed in its meandering segments. Within Dongting Lake, distinct patterns emerged. The western Dongting area was near equilibrium with no clear trend, the southern Dongting experienced significant deposition along floodways from the Three Outlets with thicknesses up to 4 meters, and the eastern Dongting exhibited complex patterns with both deep scour pits infilled by sediment and a depositional bar at the Zhuzikou inlet. Furthermore, the outlet channel in the lake-river confluence zone experienced upstream erosion and downstream deposition, gradually flattening the longitudinal slope. Regarding model validation, the simulated results closely aligned with previous studies and field observations. The deviation in total deposition was 17.0% compared to a 1D model over 30 years, and the deviation was approximately 14.2% at 10 and 20 years compared to an earlier 2D lake model. Notably, the predicted average annual deposition of 89.3 million m³ from 2011 to 2020 closely matched the measured data, further supporting the model’s reliability. [Conclusion] This study demonstrates that integrating a morphological acceleration factor into a 2D water-sediment model enables efficient and accurate simulation of decadal-scale morphodynamics in large river-lake systems. The MF method decreases computational time for a 30-year simulation by about 60%-70% while maintaining prediction errors within 5% for total lake deposition. The Jingjiang reach is projected to undergo continued incision, while Dongting Lake will experience slight net deposition at a strongly declining rate, indicating adjustment toward a new dynamic equilibrium. Spatially heterogeneous erosion-deposition patterns highlight the need for targeted management strategies.