This study investigated the effect of Pontederia cordata on Microcystis aeruginosa growth in three different experimental settings: (i) co-cultivation, (ii) exposure of cyanobacteria to culture water of P. cordata, and (iii) exposure of M. aeruginosa to organic extracts of P. cordata. Results showed that the growth of M. aeruginosa was significantly inhibited by co-cultivation, with the highest inhibition rate of 61.9% within 5 days. Moreover, 95% culture water with P. cordata could markedly inhibit the growth of M. aeruginosa, with inhibition rate of 98.3% on day 6, indicating that most of the algal cells died. The organic extracts of fibrous root showed stronger inhibition effect than the leaf and stalk extracts. Acetone extract of fibrous root showed the strongest inhibitory effect on M. aeruginosa. Different components of 80% acetone extracts from fibrous root exhibited varied effects on the growth of M. aeruginosa. Ethyl acetate and water components had strong inhibition effects on M. aeruginosa. By contrast, n-butyl alcohol components had weak inhibition effects, and hexane components even promoted the growth of M. aeruginosa. Allelochemicals of P. cordata were primarily released into the water through the fibrous root. Results indicated that P. cordata can be applied in environmentally friendly algal inhibition.