To investigate the purification effect of the new adsorption material containing bioreactor and the critical role of non-culture (VBNC) bacteria in eutrophication ecosystem, major water quality parameters and microbial community were determined and analyzed in prepared eutrophic water for 2 years monitoring. The results showed that removal rates of total phosphorus (TP), total nitrogen (TN), chlorophyll-a (Chl-a) and chemical oxygen demand (COD) ranged of 90.7% - 95.9%, 84.5% - 92.4%, 87.9% - 95.8% and 68.3% - 82.7%, respectively, indicating the designed bioreactor possessed high efficiency in eutrophic water treatment. Although the bioreactor had been operated for 2 years, water from treatment group was more clearer and odorless than control group, exhibiting the long service life of the bioreactor. Stopping operation in August caused the removal rates of major water quality parameters significantly decrease (p < 0.05), revealing stopping operation and high temperature in Summer exerted dual effect on the bioreactor, whereas the impact could be minimized when the bioreactor was running. According to most probable number (MPN) method, the total bacteria under +Rpf treatment were higher than under -Rpf treatment, implying Rpf could resuscitate VBNC bacteria in eutrophication ecosystem. Nine VBNC bacteria were isolated based on the BLAST results of 16S rRNA gene, and these bacteria might contribute to eutrophic water treatment based on their functions, such as phosphorus-collecting and denitrification. Those results provided new insights for engineering technology innovation and had benefit in eutrophic water treatment.