The purpose of this paper was to examine the effect of microbial fuel cells coupled with solar cells (MFC-SCs). In this study, MFC-SCs were constructed to understand the role of intermittent illumination in electricity generation and sediment remediation based on the sediment microbial fuel cell scenario. Furthermore, the microbial community structure on the anode in the sediment was probed using high-throughput sequencing. We identified that SCs with natural intermittent illumination (12 h per day) can promote the electricity production and nutrient utilization of the sediment of MFCs to the greatest extent, which can help manage solar energy utilization for environmental conversion and control the eutrophication of water bodies.The removal rates of NH3-N, NO3-N, organic matter and TP by the MFC-SC were 46.23% ± 1.06%, 41.50% ± 3.80%, 23.20% ± 1.40% and 24.40 ± 5.50%; in contrast, those of the traditional MFC were 25.10% ± 2.40%, 18.70% ± 4.10%, 14.10% ± 0.90% and 13.00% ± 2.50%, respectively. Meanwhile, the treatment groups in MFC-SCs influenced the species components and microflora structure. The 6329 operational taxonomic units (OTUs) in the control group without solar cells outnumbered those of the treatments of 24 h MFC-SC (5676), 12 h MFC-SC (5664) and 3 h MFC-SC (5592). This can advance the enrichment of dominant bacteria; meanwhile, the microbial process and the mechanisms behind it require further study. These results indicate that MFC-SCs provide a comprehensive method of solar energy utilization and environment remediation.