Scirpus mariqueter is a typical pioneer plant in the salt marshes of the Yangtze Estuary. A study on the morphological and biomass allocation characteristics, as well as environmental factors, of Scirpus mariqueter were carried out in fixed sampling sites in the Jiuduansha Shoals of the Yangtze Estuary. We aim to provide the scientific basis for the cultivation and restoration of Scirpus mariqueter and the utilization and protection of salt marsh ecosystems. The results showed the following:(1) among the different sites, the stembase height, corm biomass allocation rate, and ratio of rhizome to corm biomass did not show a significant difference (P > 0.05), while the shoot height, shoot density, rhizome allocation rate, fruit allocation rate, shoot biomass allocation rate, root biomass allocation rate, ratio of fruit to corm biomass, and ratio of fruit to rhizome biomass varied significantly (P < 0.05); (2) the sediment salinity, electroconductibility, bulk density (0-5 cm, 25-30 cm), total carbon content (10-15 cm, 20-25 cm, 25-30 cm), and total nitrogen content (5-10 cm) varied significantly among sites (P < 0.05); (3) only the combination of six factors, including the bulk density (0-5 cm), total carbon content (5-10 cm, 25-30 cm), total nitrogen content (0-5 cm, 5-10 cm) of the sediment, and stembase height of the plant had significant effects on the ratio of fruit to rhizome biomass of Scirpus mariqueter (P < 0.01), but the other environmental factors as well as plant morphological parameters did not show significant correlations with other biomass allocation indices. The biomass allocation characteristics of Scirpus mariqueter were the result of comprehensive effects of the plant growth characteristics and environmental factors. More factors should be included in further studies to reveal the synthetic effects of different factors on the biomass allocation of Scirpus mariqueter.