Regime shifts, usually accompanied by a decline in ecosystem quality and functions, have proven to be ecological disasters for coastal ecosystems in recent years. Shenzhen Bay is located in the core area of the Guangdong-Hongkong-Macao Great Bay, and a better understanding of its ecosystem evolution is crucial for appropriate nearshore environmental management. Four sediment cores were obtained in 2014 from the Futian mangrove wetland within the bay. Multiple sedimentary and biogeochemical proxies (including heavy metals, nutrients, grain size, and organic indicators) were analyzed to reconstruct the historical environmental changes and detect potential regime shifts in Shenzhen Bay over the past half century. The results indicate that the Futian mangrove ecosystem in Shenzhen Bay has experienced a significant shift in the early to mid-1980s. Before the shift (1954-1980), the concentrations of heavy metals, nutrients, and organic matters in core sediments stayed at low levels despite a slow increasing trend. After the shift (1990-2014), as the Shenzhen Bay received increasing pollution loadings, the concentration patterns of heavy metals and nutrients have significantly changed, resulting in a decline in ecosystem quality. The reconstructed evolution and regime shift revealed here provide scientific data for better ecosystem management and restoration strategies in the Great Bay Area.