We extend a numerical model to explore the morphodynamics of intertidal flats, with a specific focus on the sorting dynamics of sand and mud. We investigate the effect of tidal currents, wind waves, sediment properties, external sediment supply, flocculation and initial bed composition on the cross-shore profile shape and sediment sorting of intertidal flats. Consistent with existing analytical theories and benchmark simplified numerical solutions, the equilibrium cross-shore profile of intertidal flats simulated by the extended model is convex-up when tidal currents dominate and it progressively becomes concave-up when the strength of wind waves increases. The equilibrium profile is influenced by the external sediment supply which can lead to the seaward advance of intertidal flats. In line with field observations, mud tends to deposit on the upper intertidal flats when wind waves are relatively weak, while sand is mainly distributed on the middle and lower tidal flats. When wind waves are strong, both sand and mud are more easily resuspended and eroded, resulting in a noticeably concave-up profile near the high water mark. The initial bed composition (e.g., percentage of mud and sand fractions) is also found to play an important role: the intertidal flat is more convex-up in a muddier environment. Numerical modeling demonstrates that sediment properties (e.g., critical shear stress for erosion, settling velocity) and flocculation can pronouncedly influence the sediment sorting dynamics by modifying the initiation threshold and the advection distance of entrained sediments. Application of the extended model to a natural study site indicates a qualitative agreement with field observations.