A macrotidal estuary with mountain streams (MEMS) is characterized by rapidly rising and falling flood peaks and large tidal ranges and is a typical estuary type with strong flow dynamics that is found worldwide. Understanding the morphodynamic evolution of MEMSs has great significance for river management. The roles of the mountain stream river flood process and macrotides on the morphology evolution still needs further quantitative study. Taking the Oujiang Estuary as an example, the evolution mechanisms of bifurcated reaches of a MEMS are studied by analyzing the hydrologic and topographic data and using a two-dimensional numerical model for flow-sediment transport. The results show that (1) under the combined actions of runoff and macrotides, sediment transport is active and morphological evolution is intensive, the main branch and subbranch historically switch frequently, and erosion generally occurs in wet years, while deposition occurs in dry years. (2) The river flood process of mountain streams causes rapid erosion, which rises and falls rapidly with a kurtosis index (K) of approximately 2.9. There is a logarithmic relation between the sediment transport load and K. The volume of sediment transport will be 40% larger than the river flood process with K = 1.2 as for the Yangtze River. (3) Macrotides with large tidal ranges could enhance the discharge asymmetry (ψ). When the ψ is greater than 1, the side branches are dominated by flood tides. Although the current study is site specific, the results are expected to provide a valuable reference for sustainable management in similar estuaries.