A pot experiment was conducted to study the allelopathic effects of the aqueous extracts from the stem and leaf of native plant Vitex negundo on the growth and photosynthesis traits of invasive weed Eupatorium odoratum, aimed to clarify the action mechanisms of the native plant in the replacement control of the invasive weed. With the treatment of the aqueous extracts, both the plant height and the relative chlorophyll content of E. odoratum decreased, and the decrements were positively correlated the concentration of the aqueous extracts. The aqueous extracts from V. negundo stem and leaf (except for the low concentration of stem aqueous extracts) had negative effects on the leaf number, total leaf area, branch number, biomass, and relative growth rate of E. odoratum, with stronger effects of leaf extracts than of stem extracts. As compared to the control, the maximum photosynthetic rate (P_max), light saturation point (LSP), and apparent quantum yield of E. odoratum treated with the aqueous extracts all decreased, while the light compensation point (LCP) increased. The photosynthesis response curve of E. odoratum decreased with the increasing concentration of the stem and leaf extracts, suggesting that both the stem and leaf aquatic extracts of V. negundo had inhibitory effects on the photosynthesis, morphology and growth of E. odoratum, and thus, native plant V. negundo could be used as the target species for the replacement control of E. odoratum invasion in China.