Aims Previous studies have shown that silicon (Si) can affect plant growth and yield by regulating the availability of other nutrients. However, the mechanisms by which Si affects plant biomass accumulation in coastal wetlands are not well explored. Methods We conducted a sampling campaign across the whole growing season of Phragmites australis under waterlogging and drought conditions in coastal wetland, and quantified the effects of Si availability on biomass accumulation. Results Compared with drought condition, the waterlogged condition improved the utilization efficiency of nitrogen (N) and phosphorus (P) of P. australis regulated by higher Si contents. Meanwhile, the increased Si contents promoted the utilization of N and P in leaf, suggesting that the increase in Si contents optimizes the photosynthetic process. Lignin contents in P. australis decreased with the increasing Si contents, which confirmed that Si can replace structural carbon components. In addition, principal component analysis (PCA) showed aboveground biomass accumulation of P. australis was synchronized with Si accumulation, indicating that Si was a beneficial element to promote biomass accumulation. Conclusions Our study implies that increasing Si availability is conducive to biomass accumulation of P. australis in waterlogged wetlands, which will provide important scientific references for the management of coastal wetland ecosystem and the increase of global 'blue carbon' sequestration.