The Yellow River Estuary is a depositional microtidal estuary which is dominated by dynamic runoff. In the present study, based on actual measured hydrological data and remote sensing images, the evolution characteristics of the sand spit, gully, branch channels, and mouth bar of the Yellow River Estuary were analysed. It was determined that prior to 1998, the incoming flow and sediment had been large, and the deposition and extension speed of the sand spit had been relatively fast, with the mouth bar becoming highly developed. However, after 1998, the incoming flow and sediment entering the Yellow River Estuary had become significantly decreased. It was observed that erosion had occurred in the sand spit, and the mouth bar had become shrunken. Currently, there are many types of gullies and branch channels in the mouth reach area, including main channels, branch channels, flood gullies, and tidal gullies which can be transformed into each other. By establishing the relationship between the incoming sediment and the epeirogenic area, it was found that the incoming sediment level from the Yellow River Estuary of 300 million tons was the equilibrium point of the sand spit deposition and erosion, and there was an approximate linear relationship observed. The evolution characteristics of the mouth reach included two categories: persistent influencing factors and accidental influencing factors. Among those, the incoming flow and sediment were determined to be the main continuous dynamic actions, and storm surges, channel oscillations, and water-sediment regulations were considered to be accidental factors. Although the time period was short, the impacts were found to have been significant. This study’s research results potentially provide a scientific basis for the future comprehensive planning of flow path stability.