Abstract: Eight parameters which were thickness of waxy layer, proportion of pith cavity area to pith area, amount of collenchyma cell layers, thickness of collenchyma cell wall,amount of phloem fiber clusters,diameter of vessel lumen,amount of vessel clusters,thickness of phloem fiber cell wall, were used to study the adaptation of anatomical structure of the stem of Alternanthera philoxeroides (Mart.) Griseb to the changing of water in this paper, by the studied plants grown in three kinds of different habitats with water variance .The results showed that along with the changing of water, all of the parameters have significant differences; the divergent degrees of them in all habitats, in turn, are diameter of vessel lumen> thickness of collenchyma cell wall> thickness of waxy layer> proportion of pith cavity area to pith area> thickness of phloem fiber cell wall> amount of phloem fiber clusters> amount of collenchyma cell layers> amount of vessel clusters. The influence of water changing on the structure of cell walls of mechanical tissue is greater than the quantities of the cells. The variation of the structure of stem is greater in terrestrial type than in floating one. The anatomical structure of the stem of Alternanthera philoxeroides (Mart.) Griseb has both terrestrial characters and aquatic characters, and to which direction it is on earth to develop will be determined by the water conditions in habitats. In the eyes of the anatomical structure of stem, it would be a chief measure to suppress the differentiation of vessel lumen and pith cavity for harnessing the overrun of the species.