Although the runner reed (Phragmites japonicus) is known to act as an ecosystem engineer in various types of wetland ecosystems, little is known about the mechanisms underlying its interaction with neighbouring plants. We investigated the ecological characteristics (structure, growth, and associated vegetation) of P. japonicus tussocks involving associated species based on the developmental stages of P. japonicus. Vegetational characteristics, such as plant density and species richness, showed humped-back relationships with the characteristics of tussock structure (i.e., surface area and height) and P. japonicus growth, possibly indicating the effects of developmental stage on associated plant species. In particular, most vegetated tussocks were classified as late-intermediate stage, which supported the maximum number of associated species, compared to other stages. The tussock vegetation consisted of annual hygrophytes, such as Polygonum thunbergii, Lindernia micrantha, and Bidens frondosa, suggesting that P. japonicus tussocks provide a favourable microhabitat for annual hygrophytes rather than perennial hydrophytes. In conclusion, as an ecosystem engineer contributing to topographic variability, P. japonicus increases the heterogeneity of wetland vegetation by enabling annual hygrophytes to occur within wetlands dominated by perennial hydrophytes, possibly resulting in enhanced biodiversity.