The inhibitory effects of liquor cultured with Nelumbo nucifera and Nymphaea tetragona on the growth of Microcystis aeruginosa have been investigated by measuring the cell number and the chlorophyll a content of Microcystis aeruginosa of culture in the laboratory. The results showed that the inhibitory effects on the growth of Microcystis aeruginosa with different concentration of the liquor cultured with Nelumbo nucifera and Nymphaea tetragona were dissimilar, and an evident phenomenon appeared that low concentrations could promote the growth of Microcystis aeruginosa. However, the inhibitory effects on the growth of Microcystis aeruginosa with continuous liquor cultured with Nelumbo nucifera and Nymphaea tetragona were obvious, which made the algal cell almost lose the capability of photosynthesis, and the inhibitory effects of liquor cultured with Nymphaea tetragona were better than those of Nelumbo nucifera. The scale-up experiment demonstrated that the algal cell received menace and damage by measuring the activities of peroxidase (SOD) and the accumulated contents of malondialdehyde (MDA) of Microcystis aeruginosa in the co-culture. Sterilization methods influenced the algal growth inhibition experiment so that high temperature couldn't replace micropore filter, which explained that the matter excreted by Nelumbo nucifera and Nymphaea tetragona may contain thermally-instabe matter.