Ecological restoration is an important strategy to recover the degradation of coastal wetlands, to protect the biodiversity, and to enhance its ecological services. Over the past twenty years, the exotic species Spartina alterniflora has rapidly invaded the salt marshes in the Yangtze Estuary, which was formerly covered by the native species Scirpus mariqueter. A large-scale restoration project was launched to annihilate the invasive species and restore the native salt marsh vegetation in the nature reserve of Chongming Dongtan. In this study, we carried out a transplantation experiment with different sizes of the S. mariqueter patches along a tidal elevation gradient. We aimed to test the value of facilitation theory (positive intraspecific interactions to facilitate organism survival success) and stress-gradient hypothesis on salt marsh restoration for the newly formed tidal flats in Chongming Dongtan. The results showed that under a certain range of intertidal stress-gradient (above flat elevation 2.0 m), increasing size of the transplanted patches significantly enhances the survival rate and shoot density of S. mariqueter (P < 0.05). The hydrodynamic conditions on the intertidal flats were closely related to the elevation of tidal flat (P < 0.05), where the stronger hydrodynamic stress at the flat elevation below 2.0 m minimizes the positive bio-physical interactions. Our results indicated that improvement in the transplantation design of the target species might motivate the positive intraspecific interactions in coastal salt marsh restoration, resulting in a significantly higher restoration success. This study highlighted the value of the facilitation theory in coastal salt marsh restoration, provided the scientific basis and technical support to the large-scale restoration projects, and enhanced the restoration efficiency of the coastal salt marshes in the Yangtze Estuary.