Spartina alterniflora (hereafter S. alterniflora) is an exotic saltmarsh species introduced into Chinese tidal flats for coastal protection purpose. Against a background of national-scale removal of this exotic species, it is essential to investigate whether native Chinese saltmarsh species could provide a similar coastal protection function. Here, the hydrodynamic turbulence attenuation by the native species Scirpus mariqueter (hereafter S. mariqueter) and S. alterniflora was compared through in situ observation in a macro-tidal estuary, China. Our results revealed that the turbulence attenuation rates of the two species depended on inundation depth and wave-current interactions. Empirical formulas were developed to predict turbulence variations within canopies under wave-dominant and coupled wave-current conditions. This study suggests that short, flexible native saltmarsh species have the potential to perform coastal protection function similar to S. alterniflora in coastal regions dominated by wave-current coupling, highlighting the complexity of using native species to enhance coastal resilience.