[Objective] The effects of surface photovoltaic (PV) power station on the structural characteristics of water quality and phytoplankton communities in subsidence ponds in the winter were investigated in order to provide data references for the application of surface PV in coal mining subsidence waters. [Methods] Water bodies and phytoplankton communities of column PV ponds, floating PV ponds, and non-PV ponds (comparison) were sampled and investigated, and the influencing factors were analysed using Pearson correlation and stepwise regression analyses. [Results] A total of 41 species of phytoplankton were identified in the column PV sinkhole pond, 40 species of phytoplankton in the floating PV sinkhole pond, and 47 species of phytoplankton in the pond without PV sinkholes; the diatom-green-algal type dominated the species. Compared with the control sinkhole ponds, the surface PV power plant effectively reduced the light intensity and lowered the levels of electrical conductivity, total dissolved solids, oxidation reduction potential, and ammonia nitrogen in the sinkhole ponds. Similarly, the floating PV power plants reduced the chemical oxygen demand, total nitrogen (TN), and total phosphorus contents in the water body. Additionally, the column PV power plant had lower levels of the above-mentioned indicators than the floating PV power plant. The number of phytoplankton species, density, and biomass in the floating PV and column PV sinking ponds were slightly lower than those in the control sinking ponds. The values for the Shannon-Wiener diversity index, Pielou homogeneity index, and Margalef richness index were ordered as follows: no PV pond > floating PV pond > column PV pond. [Conclusion] Surface PVs can help reduce the salinity of winter water bodies and maintain both the temperature of the water bodies and the content of dissolved oxygen. The above indices used for the column PV power station to improve its effect were better than those for the floating PV power station, and to a certain extent, the floating PV power station could improve eutrophic water bodies. Surface PVs can affect the structure of phytoplankton communities, and the effect of floating PVs on the phytoplankton of sunken water bodies is smaller than that of column PVs. Pearson and stepwise regression analyses revealed that the phytoplankton community diversity of column PV sunken ponds is mainly affected by water temperature (WT) and TN, while that of floating PV subsidence ponds are mainly affected by the WT. In summary, floating PV power station are more favourable for improving the water quality of subsidence ponds and have the least impact on the phytoplankton community structure.