Silica (Si) is the second most abundant element after oxygen in the soil and plays an important role in many biogeochemical processes, such as controlling the functions of terrestrial, marine, coastal, and inland water ecosystems. Wetland ecosystems are considered very important for Si transport in nutrient biogeochemical cycles. In recent years, Spartina alterniflora has become one of the most important invasive plants in coastal wetland ecosystems in China, which has caused considerable effects on the invaded regions. The Shanyutan marsh is the largest tidal wetland in the Min River estuary in the subtropical zone of southeast China. S. alterniflora started to invade Shanyutan marsh in 2002, and since then has gradually expanded its cover across the intertidal zone. The invasion of S. alterniflora has an important impact on the cycling of carbon, nitrogen, phosphorus, and sulfur, but the effect on available silica (ASi) in the soil is not yet clear. To explore the spatial and temporal variations of ASi contents in marsh soils under the S. alterniflora invasion in Shanyutan of the Min River estuary, the Cyperus malaccensis marsh, S. alterniflora marsh, and their ecotonal marsh were studied from January to December 2016. Results showed that temporal variations of ASi contents of three different marshes generally increased with time. Compared to C. malaccensis marsh, S. alterniflora invasion significantly increased ASi contents in 30-60 cm soil layers, and values in the ecotonal and S. alterniflora marshes increased by 8.56% and 19.97%, respectively. The stepwise linear regression analyses showed that soil temperature and electrical conductivity were the crucial factors affecting the variations of ASi contents. The spatial and temporal variations of ASi contents in marsh soils are important to reveal the biogeochemical cycling of silica to better understand the invasion and expansion mechanisms of S. alterniflora in a marsh ecosystem.