Alternanthera philoxeroides has successfully invaded diverse habitats with considerably various water availability, threatening biological diversity in many parts of the world. Because its genetic variation is very low, phenotypic plasticity is believed to be the primary strategy for adapting to the diverse habitats. In the present paper, we investigated the plastic changes of anatomical traits of the aerial parts of A. philoxeroides from flooding to wet then to drought habitat; the results are as follows: A. philoxeroides could change anatomical structures sensitively to adapt to water regime. As a whole, effects of water regime on structures in stem were greater than those in leaf. Except for principal vein diameter and stoma density on leaf surfaces, all other structural traits were significantly affected by water regime. Among which, cuticular wax layer, collenchyma cell wall, phloem fiber cell wall, and hair density on both leaf surfaces thickened significantly with decrease of water availability, whereas, pith cavity and vessel lumen in stem lessened significantly; wet habitat is vital for the spread of A. philoxeroides from flooding to drought habitat and vice versa, because in this habitat, it had the greatest structural variations; when switching from flooding to wet then to drought habitat, the variations of cuticular wax layer, collenchyma cell wall, phloem fiber cell wall, pith cavity area ratio, diameter of vessel lumen, and hair density on both leaf surfaces, played the most important role. These responsive variables contribute most to the adaptation of A. philoxeroides to diverse habitats with considerably various water availability.