The ecological floating bed system (EFBS), as an effective means to improve the water quality and restore water ecosystem, was widely applied by worldwide scientists. Biomass and the community structure of phytoplankton are important characters of the water eutrophication. The effect of two EFBSs, a new EFBS with sufficient space in surface, equipped with zeolite, and the traditional foam EFBS, on water quality and phytoplankton community was employed to investigate the response of phytoplankton to EFBS during the process of water quality restoration. A terrestrial plant Cyperus alternifolius and the water from a canal nearby were tested in the present study. Treatments included Control with no phytoplankton, the traditional EFBS and the new EFBS. Nutrient concentration in water and phytoplankton were detected at two weeks interval during the two months experimental time. The results showed that after the canal water was transported to the experimental concrete cistern for 2 weeks, Chlorella Beij. and Scenedesmus Mey., which belong to Chlorophyta, came to dominate the phytoplankton population, insteading of Oscillatoria Vauch. and Spirulina Turp., which belong to Cyanophyta due to the habitat alteration. Simultaneously, total biomass of phytoplankton decreased rapidly from 20mg/L to below 3mg/L. At most of the experimental time, the biomass of phytoplankton under both EFBS treatments was significantly lower than that in Control (P<0.05) with a decreasing order of control>traditional EFBS>new EFBS. A water bloom composed of Microcystis Kütz broke out in Control after one and half months and it highest abundance and biomass reached 80.22×106ind./L and 5.21mg/L. Both EFBS could significantly remove all forms of N and P (P<0.05), especially NH4-N and TP (P<0.01) in water, and the new EFBS showed better effect than the traditional EFBS. The positive correlation between phytoplankton biomass and nutrients level, especially with TP (0.579, P<0.05) and TDP (0.611, P<0.05) indicated that EFBS might affect phytoplankton indirectly through removing nutrients from water, and the high efficiency of P removal by EFBS could be the main contribution of EFBS in controlling water bloom.