The phytoplankton community in Qiandao Lake has typical seasonal succession characteristics, and Cyanophyta, especially the genus Microcystis, are dominant in summer. To evaluate the control effects of filter-feeding fish (silver carp and bighead carp) on cyanobacterial blooms, the changes in algal species composition along the fish intestine were analyzed by microscopic examination, chlorophyll fluorescence, high-throughput DNA sequencing and pigment ratios. The microscopic examination results showed that both silver carp and bighead carp have a certain control effect on bloom-forming cyanobacteria in spring. The digestion of silver carp in summer could still effectively remove cyanobacteria and reduce the dominance of Microcystis in the phytoplankton community, while the digestion of bighead carp seemed to have little effect on cyanobacteria. The results of the chlorophyll fluorescence method were similar to those of the microscopic analysis, which indicated that silver carp could reduce the cyanobacterial biomass in spring, while bighead carp could significantly promote the dominance of cyanobacteria (p < 0.001). High-throughput DNA sequencing showed that there were significant differences in filter-feeding plankton between silver carp and bighead carp. The midgut may be the main gathering site of intestinal microorganisms, and cyanobacterial digestion mainly occurs in the intestinal segments between the foregut and midgut. The analysis of pigment ratios indicated that selective digestion of phytoplankton by silver carp significantly reduced the dominance of Cyanophyta in its hindgut (p < 0.01), while bighead carp had the opposite effect (p < 0.05), especially in seasons other than spring. The results of the above four methods are basically the same, that is, the digestion effect of silver carp on cyanobacteria is better than that of bighead carp. Therefore, the stocking proportion of silver carp should be appropriately increased in some meso-eutrophic waterbodies.