Model input reduction and morphological acceleration techniques to bridge the large time scale of morphological evolution and the small time scale of hydrodynamically driven sediment transport is investigated for the Yangtze Estuary morphodynamic model. The discharge series of the river is schematized into a set of multi-discharge levels. Each discharge level coupled with the spring-neap tide forms one morphodynamic model for the estuary with bed stratigraphy approach applied. These models are used to simulate the bathymetry change of the estuary in parallel with the results merged together base on the Mor-Merge (MM) method. The morphological factor is used to accelerate the bathymetry change during hydrodynamic simulation. The modelled bathymetry change based on MM method is compared with the Quasi Real Time (QRT) simulation result. It shows that the results of the MM model with more discharge levels correlate more significantly with that of the QRT model. Therefore, the MM approach with multi discharges, which achieves an acceptable acceleration for morphological change, results in the feasibility of the medium term morphodynamic model of the Yangtze Estuary.