Abstract: Aqueous extracts of the root, stem and leaf of cord grass Spartina alterniflora at concentrations of 0.325g/cm³ were used as treatment solutions to study the allelopathic effect of exotic S. alterniflora on native Cyperus malaccensis in Minjiang Estuary. Results showed that different aqueous extracts had different allelopathic effects on different growth and physiological indices. For 3 month treatment, the inhibition of the extracts on the C. malaccensis’s tiller number and leaf area showed significant difference and extremely significant difference, respectively. The inhibition of the root and stem extracts on the C. malaccensis’s root activity both showed significant difference. Allelopathic effect of the leaf extracts on C. malaccensis was stronger than root and stem.