Abstract: The quality of estuarine environments is of paramount importance to coastal ecosystems and sustainable development. Xiamen Bay has undertaken extensive comprehensive restoration and ecological rehabilitation efforts in 2000-2020, however no studies have systematically revealed the changes in marine environmental quality over these twenty years. Used time-series data from time nodes of 2000, 2010 and 2020, 5 indexes, dissolved oxygen, inorganic nitrogen, and reactive phosphates in the seawater, organic carbon and sulfides in the sediments were selected as indexes to assess the spatiotemporal changes of the marine environmental quality based on the entropy-weighted TOPSIS model. Results indicate that all indexes increased at rates of 1.2% to 11.8% from 2000 to 2020, overall, the improvement in water quality indexes was greater than that of sediments, of which the organic carbon index showed the least improvement. The standard deviations of most indexes decreased with time, suggesting a trend of more stable marine environmental quality. The comprehensive marine environmental quality index exhibited an increasing trend with time with 45.42% of the areas showing improved environmental quality, while only 14.67% areas went slight declining mostly concentrated in Jiulong River Estuary. Spatially, the comprehensive index in all three time nodes showed lower in the west and higher in the east, indicating that the eastern part of Xiamen Bay had consistently better marine environmental quality than the western part. Spearman correlation analysis indicates that the dominant driving factors changing the marine environmental quality of Xiamen Bay water are inorganic nitrogen, active phosphate and sulfides. This study provides valuable insights into the spatiotemporal changes of marine environmental quality and offers a scientific basis for marine ecological environment management and protection in Xiamen.