Cyanobacterial blooms in eutrophic lakes have significant influence on population and community structures of cladoceran, but the impacts of natural colonial Microcystis spp. on the growth and reproduction of Daphnia remain controversial. Two 10-day experiments were conducted separately to simulate the impacts of the colonial Microcystis spp. (20 100 μm and 100 200 μm) on population characteristics of D. similis, which were cultivated in filtered water from Lake Taihu. The results show that colonial Microcystis spp. has no significantly negative effect on the survivorship of D. similis. The growth rate and reproductive capacity of D. similis differed among different concentrations and sizes of colonial Microcystis spp., which was significantly higher in groups with Microcystis than the control group. Our results indicate that there is no significant inhibition from cellular microcystins on the population of D. similis in natural conditions. D. similis can coexist with Microcystis blooms and its population characteristics are mostly affected by the size composition and biomass of colonial Microcystis spp.