The study of dark carbon fixation in estuarine wetlands is of great scientific significance for the comprehensive understanding and scientific assessment of the carbon sink potential of estuarine wetlands. Taking Chongming Dongtan as a typical study area,the effects of different wetland vegetation distributions on sediment dark carbon fixation and its key environmental control factors were studied using ¹⁴C isotope labeling technology combined with molecular biology research methods.The results showed that: the annual mean values of sediment dark carbon fixation rates in mudflat, Phragmites australis, and Spartina alterniflora wetlands were (1.27±0.66),(0.88±0.40),(1.37±0.63) mmol/(m²·d) C, respectively; there were significant seasonal differences in sediment dark carbon fixation in estuarine wetlands, in which the dark carbon fixation rates increased significantly in summer, but were inhibited by extremely high temperatures; the dark carbon fixation in sediments was promoted by Spartina alterniflora, while that in the Phragmites australis area was reduced relative to the mudflat; different vegetation influenced the dark carbon fixation in the sediment by regulating the NH⁺₄, Fe³⁺, S^2- and the abundance of functional genes (cbbL and cbbM). The results provide a theoretical reference to accurately assess the carbon sink potential and the influence mechanisms of the estuarine wetlands.