The spatiotemporal changes of inundation frequency in the Yellow River Delta (YRD) have profound influences on sustainable ecological protection and are also closely relevant to economic development scarcity on the coast of China. However, long-term changes of inundation frequency have remained poorly characterized. Using the Google Earth Engine (GEE) cloud platform, this study processed Landsat images to explore inundation frequency changes from 1990 to 2020 in the YRD. The results indicated that (1) The existing water index combining the classification results based on the MLM (Maximum Likelihood Method) is suitable for the mapping of the long-term water bodies, especially in the coastal regions; (2) The inundation frequency showed a clearly uneven temporal–spatial distribution. The low inundation area (LIA) is mainly intertidal natural wetlands with a declining trend, while the high inundation area (HIA) is dominated by constructed wetlands with a rising trend; (3) The use frequency of artificial ponds determines the inundation frequency of the constructed wetland. The industry development has gradually matured, causing the inundation frequency from dispersion to concentration in the constructed wetland; and (4) In the natural wetland, the LIA have increased since 2010 and have accounted for 30% in 2020. The large-scale appearance of LIA occurs with the emergence of high vegetation abundance. Spartina alterniflora salt marshes with strong reproductive ability and high abundance lead to the difficulty of wetland flooding and reduce the inundation frequency.