Heterogeneous environment affects the distribution and diffusion of species at different ecological levels, which may thus significantly affect the invasion situation of alien species. Here, we analyzed the structure characteristic of aquatic invasive Alternanthera philoxeroides community and divided its association types based on 23 sampling plots (10 m × 10 m) spanned from 21°N-31°N in China, by using the method of twoway indicator species analysis (TWINSPAN) and detrended correspondence analysis (DCA). Meanwhile, we also analyzed the relationships among species distribution, population characteristics of A. philoxeroides and various environmental factors using redundancy analysis (RDA) to provide references for biological invasion control and native biodiversity protection. The results showed that: (1) 23 plots recorded 48 plant species, which belonged to 21 families and 42 genera, A. philoxeroides had the largest dominance, the dominant accompanying species were Paspalum paspaloides, Leersia hexandra, Polygonum hydropiper. (2) 23 plot communities were divided into 6 associations, among those, A. philoxeroides + P. paspaloides + Oenanthe javanica was the main association type. (3) 48 plant species were divided into 4 functional groups, including pioneer species group, dominant accompanying species group, secondary companion species group, and avoiding species group. The DCA differentiation of functional groups was larger than that of association types. (4) Species distribution was mainly determined by ammonia and conductivity of waters. However, species richness and population characteristics of A. philoxeroides were multiply influenced by conductivity, longitude, elevation and dissolved oxygen. Additionally, the aquatic A. philoxeroides invasion situation was largely depended on its asexual branch numbers and coverage. Our research clearly indicates that the structure of aquatic invasive A. philoxeroides community is relatively simple. We should intensify the invasion monitoring and maintain higher habitat heterogeneity, for alleviating the invasion progress in aquatic ecosystems.