A physic-ecological engineering (PEEN) for aqua-eco-remediation was performed in a local area (enclosed water with surface area of 1.33 ha) with depth round 10 m and variation of water level of 7 m in Lake/Reservoir Hongfeng. Results showed that the construction, abundance and biomass of the phytoplankton may be regulated by PEEN, when the ratio of the sum area of floating islands with plant to the total enclosed area is above 1/5-1/3(as the threshold). The dominant phytoplankton population shifted from Cyanophyta (Microcystis), Pyrrophyta (Ceratium hirundinella) and Cyanophyta (Dactylococcopsis acicularis) in surrounding algae-type water to Bacillariophyta (Melosira) after the construction of engineering. Species of Cyanophyta in plant-type water were less than that of surroundings at 17.6%-29.4% (especially the species with microcystin, such as Microcystis, Anabaena, Oscillatoria, Aphanizomenon, were detected in surroundings algae-type water did not been detected in plant-type water); while the species of Bacillariophyta increased to 120.0% in comparison with that in the surroundings. The abundance and biomass of Cyanophyta in the plant-type area of the PEEN decreased by 55.5% and 57.9% in comparison with those in surroundings, respectively. Meanwhile, the abundance and biomass of Bacillariophyta in the plant-type area of the PEEN increased by 56.4% and 60.3% in comparison with those in surroundings, respectively. The total phytoplankton abundance and biomass decreased by 53.6% and 39.1%, respectively in comparison with those of the surroundings. All these facts benefited the increase of transparency in plant-type water, where the water quality improved obviously and the secchi depth is stably observed at 120-220 cm and higher than that in surrounding algae-type water in dozen centimeters. The engineering area appears as the "green island" in the algae bloom occupied surroundings frequently. The eutrophication in local area of Lake Hongfeng with surface area of 57.2 km² at normal water level is controlled without algae bloom. The PEEN including floating eco-islands, which can be used for culturing various water surface plant, including aquatic plant, wetland plant, terrestrial plant (Vetiver Grass, salix integra linn., etc), for relieving high wind-driven wave, suppressing blue algae, improving water quality and transparency and other techniques is important for guaranteeing the remediation of submerged vegetation in shallow lakes and preventing algae bloom under severe environmental pressure at present.