Biological controls of phytoplankton are divided into traditional biomanipulation using zooplankton and nontraditional biomanipulation using filter-feeding fishes, and the former theory developed by western scholars are suitable for controlling small algae, while the latter one developed by Chinese scholars are effective for controlling colony-forming cyanobacteria (especially Microcystis). Lake Donghu is a eutrophic lake, located in Wuhan City, China, with a surface area of ca. 32 km². Before 2021, cyanobacterial blooms had been absent from the main part of the lake (Guozhenghu area, 12.8 km²) for more than 30 years. However, in the summer of 2021, Microcystis blooms suddenly occurred in the lake, with a maximum coverage of approximately 87%. After examining the long-term monitoring data of the Donghu Experimental Station of Lake Ecosystems, we found that current nutrient (nitrogen and phosphorus) levels are still high enough for the outburst of cyanobacterial blooms in this lake. As it is impossible to efficiently decrease the nutrients within a short period of time (e.g. a couple of years), non-traditional biomanipulation (using the native filter-feeding silver and bighead carps with an appropriate abundance) was applied to counteract the occurrence of cyanobacterial blooms, and as a result, no blooms were present in 2022 in spite of an extremely hot and dry summer, i.e., the Lake Donghu ecosystems was shifted quickly from a bloom steady state to a non-bloom one, demonstrating a new regime shift, and achieving a success that the traditional biomanipulation had never had before. Conclusively, the non-traditional biomanipulation theory was tested and validated using a whole lake experiment, providing an environmentally friendly, extremely low-cost and rather effective way to control colony-forming cyanobacterial blooms in eutrophic lakes.