Tracking long-term tidal flat dynamics is crucial for coastal restoration decision making. Accurately capturing the loss and gain of tidal flats due to human-induced disturbances is challenging in the micro-tidal areas. In this study, we developed an automated method for mapping the annual tidal flat changes in the micro-tidal areas under intense human activities, by integrating spectral harmonization, time series segmentation from dual spectral indices, and the tide-independent hierarchical classification strategy. Our method has two key novelties. First, we adopt flexible temporal segments for each pixel based on the dual full-time series spectral indices, instead of solely using a fixed period window, to help obtain more reliable inundation frequency features. Second, a tide-independent hierarchical classification strategy based on the inundation features and the Otsu algorithm capture the tidal flat changes well. Our method performed well in Guangdong, Hong Kong, and Macao (GHKM), a typical area with micro-tidal range and intense human activities, with overall accuracies of 89% and 92% for conversion types and turning years, respectively. The tidal flats in GHKM decreased by 24% from 1986 to 2021, resulting from the loss of 504.45 km2, partially offset by an accretion of 179.88 km2. Further, 70.9% of the total loss was in the Great Bay Area, concentrated in 1991–1998 and 2001–2016. The historical trajectories of tidal flat loss were driven by various policies implemented by the national, provincial, and local governments. Our method is promising for extension to other micro-tidal areas to provide more scientific support for coastal resource management and restoration.