Sediment composition, characterized by different contents of cohesive and non-cohesive sediments, is known to play a role on long-term estuarine and deltaic morphodynamics, but the exact impact is poorly understood. We establish a two-dimensional morphodynamic model to investigate the influence of different sediment compositions on the development of a schematic fluvio-deltaic system driven by river and tides. Though excluding the density effects, results suggest that the model captures the development of distributary channels and elongated sand bars with resemblance to that in the Yangtze Estuary. Sensitivity simulations show fundamentally different channel-shoal patterns take shape under different sediment compositions. Ebb dominance and associated seaward sediment flushing lead to faster morphodynamic development and more prograded delta under larger river discharge and sediment supply. We detect a positive correlation between the content of cohesive sediment and the speed of development, particularly cohesive sediment content is <50%. However, when the proportion of mud is larger (i.e., 50–75%), a deceleration of the morphological development occurs after 200 years. A sand-dominated environment exhibits the largest channel numbers and fast channel formation near the mouth within the first 300 morphodynamic years. Spatial distribution of bottom sediments changes with morphology, exhibiting increasing mud deposits near the mouth, whilst the sand remains inside the estuary. This study indicates the importance and need for a more realistic representation of bed compositions in long-term estuarine morphodynamic simulations.