Many exotic invasive aquatic plants are clonal plants, but the investigations on the influence of clonal integration on the potential invasive effects of these plants are still limited. This study investigated clonal integration(stolon connection) and simulated sedimentation burial(3 cm sediment burial) on the growth, antioxidase activity and biomass allocation of the invasive aquatic macrophyte, Myriophyllum aquaticum, to explore the clonal integration effect on the tolerance mechanism of this species. We found that:sediment burial significantly reduced the final biomass, total stolon length and branch number, whereas these growth measures of the ramets buried by sediment were markedly improved by stolon connection. The antioxidase activities(superoxide dismutase, peroxidase and catalase) of the buried ramets were significantly lower than that in the control group, whereas those values were remarkably enhanced by clonal integration. Moreover, clonal integration significantly reduced the shoot/root ratio of those sediment buried ramets. The obtained results suggest that, under the stress of the sediment burial, clonal integration can enhance the reactive oxygen species scavenging ability of M. aquaticum ramets, thus improving their growth. Moreover, clonal integration can change the biomass allocation of the ramets, allowing them to acquire more abundant resources. Therefore, we conclude that the invasiveness of the M. aquaticum may be closely related to its clonal integration characteristic under heterogeneous environmental stresses.