In recent years, the shrinkage of Poyang Lake, the largest freshwater lake in China, has raised concerns for society. The regulation of the Three Gorges Dam (TGD) has been argued to be a cause of the depletion of the lake by previous studies. However, over the past few decades, the lake’s surface water dynamic has remained poorly characterized, especially before the regulation of the TGD (2003). By calculating the inundation frequency with an index- and pixel-based water detection algorithm on Google Earth Engine (GEE), this study explored the spatial–temporal variation of the lake during 1988–2016 and compared the differences in Poyang Lake’s water body between the pre- and post-TGD periods. The year-long water body area of the lake has shown a significant decreasing trend over the past 29 years and has shifted to a smaller regime since 2006. The inundation frequency of the lake has also generally decreased since 2003, particularly at the central part of the lake, and the effects of this trend have been most severe in the spring and autumn seasons. The lake’s area has shown significant correlation with the precipitation of the Poyang Lake Basin on an inner-annual scale. The drivers of and relevant factors relating to the inter-annual variation of the lake’s surface water should be further investigated in the future.