Salt marshes are the transition zones of land and ocean which are intertidal ecosystem dominated by large herbaceous plants. The floating initiation of salt marsh seeds and seedlings under the tidal current is an important prerequisite for the natural dispersal of saltmarsh plants in the intertidal ecosystem, which determines whether saltmarsh plants can disperse effectively over long distance. Unfortunately, there are few quantitative studies on the floating initiation and diffusion of salt marsh propagules in the complex tidal flat environment. Here, we focused a typical saltmarsh pioneer species Scirpus mariqueter in the Yangtze estuary, aiming to explore the critical shear stress of floating initiation for S. mariqueter seeds and seedlings at the different germination stages and on the different sediment substrates. The critical shear stress of floating initiation for S. mariqueter seeds and seedlings under experimental gradients were measured by U-GEMS micro erosion system, and the effects of different germination stages and sediment substrates on the floating initiation of S. mariqueter seeds and seedlings were quantitatively analyzed. The results showed that:(1) the germination stages and sediment substrates had significant effects on the critical shear stress of floating initiation for S. mariqueter seeds and seedlings (P < 0.01); (2) the critical shear stress of floating initiation for S. mariqueter seedlings decreased gradually with the increase of germination stage, and the chance of dispersal with tidal current increased accordingly; (3) compared with the sediment substrate of muddy tidal flat, the seeds and seedling of S. mariqueter were easier to float in the silty tidal flat. This study enhances the understanding of the process and mechanism of saltmarsh natural dispersal, and provides a scientific basis for efficient low-cost and large-scale saltmarsh restoration in the Yangtze estuary and other regions using seeds as restoration materials, which has important theoretical significance and practical application prospects.