Our study investigated the characteristics of Phragmites australis (Gramineae) silicon (Si) accumulation, and the response relationship between P. australis Si accumulation and groundwater depth changes. Plants were dug out and taken back to the laboratory for Si accumulation analysis, and a supplementary survey of P. australis Si accumulation was conducted among different groundwater depths. Result showed that Si absorbed and accumulated by P. australis mainly came from the soil and the Si accumulation differed significantly in tissues and growth stages, and the total Si accumulations (withering stage) of P. australis in sand dune (SD), desert steppe (DT), interdune lowland (IL), saline meadow (SM), and wetland (W) habitats were 7.09%, 6.77%, 5.72%, 7.73%, and 8.12%, respectively. More importantly, P. australis Si accumulation was almost equal to the total accumulation of nitrogen, phosphorus, and potassium, and even higher than of the total accumulation of calcium, magnesium, and sulfur. P. australis Si accumulation (withering stage) reduced first from SD to DT habitat, and then increased remarkably from DT to W habitat with a significant increase of -23.95% and 41.96%, respectively. P. australis Si accumulation positively responds to the groundwater depths, and the relationship was an increasing linear function of one variable. Our findings suggested that accumulating Si might be one of the effective strategies for P. australis to adapt to adverse habitats, and the Si-rich characteristic of P. australis was likely to lay a solid theoretical foundation for exploring effective measures to restore and reconstruct the degraded ecosystems in desert oasis areas.