As an internationally important wintering region for waterfowls on the East Asian–Australasian Flyway, the national reserve of China’s East Dongting Lake wetland is abundant in animal and plant resources during winter. The hydrological regimes, as well as vegetation dynamics, in the wetland have experienced substantial changes due to global climate change and anthropogenic disturbances, such as the construction of hydroelectric dams. However, few studies have investigated how the wetland vegetation has changed over time, particularly during the wintering season, and how this has directly affected habitat suitability for migratory waterfowl. Thus, it is necessary to monitor the spatio-temporal dynamics of vegetation in the protected wetland and explore the potential factors that alter it. In this study, the data set of time-series Moderate Resolution Imaging Spectroradiometer (MODIS) normalized difference vegetation index (NDVI) from 2000 to 2018 was used to analyze the seasonal dynamics and interannual trends of vegetation over the wintering period from October to January. The results showed that the average NDVI exhibited an overall increasing trend, with the trend rising slowly in recent years. The largest monthly mean NDVI generally occurred in November, which is pertinent to the quantity of wintering waterfowl in the East Dongting Lake wetland. Meanwhile, the mean NDVI in the wintering season is significantly correlated to temperature and water area, with apparent lagging effects. Long-term stability analysis presented a gradually decreasing pattern from the central body of water to the surrounding area. All analyses will help the government to make appropriate management strategies to protect the habitat of wintering waterfowl in the wetland.