Due to a steep slope, rapid flow, and large amounts of sediment, rivers in Taiwan are braided rivers that are full of bars and bifurcated flows. The channel shifting behavior and bar migration within natural braided rivers results in difficult river engineering. In this study, the Nays2DH model was used to simulate the braiding processes and morphological changes downstream of Shigang Dam in the Da-jia River from 2012 to 2013. Furthermore, the characteristics of riverbed erosion, the stability of the channel in the longitudinal and transverse directions and the impact of river structures on the morphology were simulated. The numerical model can present morphological and evolutionary processes similar to an actual river, such as: central bar formation, chute cutoff, and channel avulsion. The scour pool mostly occurred at the apex of the river bend and downstream of the bar (confluence) in a braided river, which means that bar migration is the main factor that alters scour position. Under the assumption of equilibrium sediment transportation across the upstream inflow section, the width of the channel determines whether the river demonstrates longitudinal erosion or transverse changing. Results from this research can be used as a substantial reference for future research concerning river morphology evolution, river engineering, and river space planning.