Invasive Spartina spp. mostly colonizes a bare tidal flat and then establishes a new vegetated habitat, where it promotes the productivity of local ecosystems. However, it was unclear whether the invasive habitat could well exhibit ecosystem functioning, e.g. how its high productivity propagates throughout the food web and whether it thereby develops a high food web stability relative to native vegetated habitats. By developing quantitative food webs for a long-established invasive Spartina alterniflora habitat and adjacent native salt marsh (Suaeda salsa) and seagrass (Zostera japonica) habitats in China's Yellow River Delta, we investigated the distributions of energy fluxes, assessed the stability of food webs, and investigated the net trophic effects between trophic groups by combining all direct and indirect trophic interactions. Results showed that the total energy flux in the invasive S. alterniflora habitat was comparable to that in the Z. japonica habitat, whereas 4.5 times higher than that in the S. salsa habitat. While, the invasive habitat had the lowest trophic transfer efficiencies. Food web stability in the invasive habitat was about 3 and 40 times lower than that in the S. salsa and Z. japonica habitats, respectively. Additionally, there were strong net effects caused by intermediate invertebrate species in the invasive habitat rather than by fish species in both native habitats. This study revealed the contradiction between the promotion of energy fluxes and the decrease of food web stability resulting from the invasion of S. alterniflora, which provides new insights into the community-based management of plant invasions.