Silicon is one of the important components of the element cycle in wetland systems, and its distribution characteristics in the soil are closely related to the activity of the soil-plant systems in wetlands. To investigate the variation in total silicon content and storage in soils in typical vegetation communities and ecotones in the Min River Estuary, the Cyperus malaccensis marsh, Spartina alterniflora marsh, and their ecotones (C. malaccensis-S. alterniflora marsh) were studied from January to December 2016 using field sampling and laboratory experiments. The results showed that the average annual silicon content in soils in the C. malaccensis marsh, C. malaccensis-S. alterniflora marsh, and S. alterniflora marsh were 197.67, 201.21, and 210.33 mg/g, respectively, and increased gradually from the land to the sea. The total silicon content in soils in different types of marshes in autumn and winter were higher than those in spring and summer. The total silicon content and storage in soils in different types of marshes in the upper layer (0-30 cm) were higher than those in the lower layer (30-60 cm). Statistical analysis showed that the total silicon content of wetland soils was significantly negatively correlated with the amount of organic matter (P < 0.05) and positively correlated with moisture and pH (P < 0.01). In addition to the C. malaccensis marsh, there was a significant negative correlation between the total silicon content and available silicon content in the C. malaccensis-S. alterniflora marsh and S. alterniflora marsh (P < 0.05). The study of the total silicon content and distribution characteristics in wetland soils in different vegetation zones in the Min River Estuary revealed that the changing in total silicon content in wetland was under the influence of different types of wetland vegetation growth and provided key data for silicon research in this study area.