The numerical simulation of non-uniform sediment transport under tidal flow in estuaries is a complicated, yet important, issue in Zhejiang estuaries. In this paper, a depth-averaged two-dimensional (2D) mathematical model for non-uniform sediment transport in estuaries is established and applied in Zhejiang tidal estuaries based on several newly derived formulas by Zhlin Sun et al. The model is validated using data from several experiments, including an aggradation test and an erosion test. Good performance in the tests indicates that the present model can simulate aggradation and erosion processes of non-uniform sediment. The model is also verified by observational data from the Jiaojiang estuary, and calculations agree well with measurements. The model is thus adaptable to simulating flow and non-uniform sediment transport in tidal estuaries.