The spatial distribution pattern of plants often reflects their ecological adaptation strategy and is formed by their long-term interaction with environmental factors. In this paper, the clonal plant, Phragmites australis, was investigated across environmental gradients, including the wet zone, the transitional zone and the desert zone of the salt marsh wetland of Dunhuang, China. The characteristics and influencing factors of their fine-scale spatial distribution patterns were studied by point pattern analysis, redundancy analysis and simple linear regression. The results show that: (1) the spatial distribution pattern of Phragmites australis changes from aggregation to non-aggregation (random and regular distribution) from the wet zone to the desert zone. (2) The soil water content, pH and salinity all affect Phragmites australis’ spatial distribution intensity. Simple linear regression reveals that the water content in each soil layer, the pH of the deep soil layer and the salinity of the surface and deep soil layers are the main soil conditions of Phragmites australis’ spatial distribution pattern. (3) Phragmites australis’ population characteristics and clonal characteristics also have significant effects on its spatial distribution intensity. Specifically, the intensity of its spatial distribution pattern is significantly positively correlated with its cover, frequency, density, height, biomass, node number, ramet number and stem diameter (p < 0.01), while it is significantly negatively correlated with its rhizome internode length, spacer length and branch angle (p < 0.01). This research clarified the relationship between the spatial distribution pattern of Phragmites australis with soil environmental factors, plant clonal characteristics and population characteristics. The results provide a theoretical basis for understanding the ecological adaptation mechanism of clonal plants and protecting the sustainability of fragile and sensitive inland river wetland ecosystems.