Numerical models provide considerable assistance in the investigation of complicated processes in natural rivers. In the present study, a physics-based two-dimensional model has been developed to simulate the braiding processes and morphodynamic changes in braided rivers. The model applies the basic hydrodynamic and sediment transport principles with bed morphology deformation and a TVD (Total Variation Diminishing) scheme to predict trans-critical flows and bed morphology deformation. The non-equilibrium transport process of graded bed load sediment is simulated, with non-uniform sediments, secondary flows, and sheltering effects being included. A multiple bed layer technique is adopted to represent the vertical sediment sorting process. The model has been applied to simulate the bed evolution process in an experimental river with bed load transport. Comparisons between the experimental river and predicted river are analysed, including their pattern evolution processes, important braiding phenomena, and statistical characteristics. Avulsion activities have been found in the braiding evolution process, representing the primary ways in which channels form and disappear in braided rivers. The increases in the active braiding intensity and total braiding intensity show similar trends to those observed in the experimental river. Statistical methods are applied to assess the scale-invariant topographic properties of the simulated river and real rivers. The model demonstrated its potential to predict the morphodynamics in natural rivers.