Results of the greenhouse experiment showed that fresh and saline water alternation irrigation had significant effects on morphological traits, clonal characteristics, biomass accumulation and biomass allocation patterns of Spartina anglica coming from the Xinyang Harbor in Jiangsu Province, China. Six irrigation treatments were set up in our experiments including single irrigation with freshwater (D) or salt water(X), single alternating irrigation with freshwater and saltwater (DX and XD) and double alternating irrigation (DXD and XDX). With the DX treatment, plant height, number of leaves and the length of roots reached the maximal value. Meanwhile, the number of ramets was significantly higher than those of X, DXD and XDX treatments (P < 0.05); the number of buds and total rhizome length were significantly higher than those of XDX treatment (P < 0.05). Roots biomass, below\|ground biomass and total biomass under DX and D treatments were both significantly higher than those of other treatments (P < 0.05). The results showed that S. anglica populations grew better with the DX treatment, which did good to sustain and regenerate the population. Not only X treatment but also excessive alternative irrigation of fresh and saline water worked against the growth and biomass accumulation of Spartina anglica. The results indicated that the frequent change in fresh and saline water for S. anglica vegetation area would explain the decline of its populations over its range.