Subsidence waterbodies play an important role in carbon cycle in coal mining area. However, little effort has been made to explore the carbon dioxide (CO₂) release characteristics and influencing factors in subsidence waterbodies, especially under different restoration modes. Here, we measured CO₂ release fluxes (F(CO₂)) across Anguo wetland (AW), louts pond (LP), fishpond (FP), fishery-floating photovoltaic wetland (FFPV), floating photovoltaic wetland (FPV) in coal mining subsidence area, with unrestored subsidence waterbodies (SW) and unaffected normal Dasha river (DR) as the control area. We sampled each waterbody and tested which physical, chemical, and biological characteristics of water and sediment related to variability in CO₂. The results indicated that F(CO₂) exhibited the following patterns: FFPV> FPV> FP> SW> DR> LP> AW. Trophic lake index (TLI) and microbial biomass carbon content (MBC) in sediment had a positive impact on F(CO₂). The dominant archaea Euryarchaeota and Thaumarchaeota, and dominant bacteria Proteobacteria promoted F(CO₂). This study can help more accurately quantify CO₂ emissions and guide CO₂ future emission reduction and subsidence waterbodies estoration.