The identification of ecosystem types is important in ecological environmental assessment. However, due to cloud and rain and complex land cover characteristics, commonly used ecosystem identification methods have always lacked accuracy in subtropical urban agglomerations. In this study, China’s Guangdong–Hong Kong–Macao Greater Bay Area (GBA) was taken as a study area, and the Sentinel-1 and Sentinel-2 data were used as the fusion of active and passive remote sensing data with time series data to distinguish typical ecosystem types in subtropical urban agglomerations. Our results showed the following: (1) The importance of different features varies widely in different types of ecosystems. For grassland and arable land, two specific texture features (VV_dvar and VH_diss) are most important; in forest and mangrove areas, synthetic-aperture radar (SAR) data for the months of October and September are most important. (2) The use of active time series remote sensing data can significantly improve the classification accuracy by 3.33%, while passive time series remote sensing data improves by 4.76%. When they are integrated, accuracy is further improved, reaching a level of 84.29%. (3) Time series passive data (NDVI) serve best to distinguish grassland from arable land, while time series active data (SAR data) are best able to distinguish mangrove from forest. The integration of active and passive time series data also improves precision in distinguishing vegetation ecosystem types, such as forest, mangrove, arable land, and, especially, grassland, where the accuracy increased by 21.88%. By obtaining real-time and more accurate land cover type change information, this study could better serve regional change detection and ecosystem service function assessment at different scales, thereby supporting decision makers in urban agglomerations. © 2022 by the authors.