Root morphology and biomass allocation are important features for determining the capacity of root absorption, and the nature of the responses to environmental constraint factors and adaptation strategies have been a hot research topic. However, numerous uncertainties about the effects of soil salinity on the root traits of plants still exist. This study was performed on Phragmites australis community in Qinwangchuan National Wetland Park of Lanzhou. Three different plots with a soil salinity gradient (plot I, Ⅱ, and Ⅲ) were set up from the edge to the center of wetland, which was perpendicular to the bank of the Sha River. The change characteristics of the morphological parameters such as the ratio of root to shoot, total and specific root lengths, root forks, and the average root diameter of P. australis were studied using the combined method of total root excavation along with the Win-RHIZO root analyzer. The results showed that the height, coverage, density, and above-ground biomass of the wetland community decreased gradually with the increase of soil salinity. In addition, the ratio of root to shoot and root forks of P. australis decreased gradually, and the specific and total root lengths of P. australis first decreased and then they subsequently increased whereas the average root diameter showed an opposite trend. The soil salinity was dominated by moderate salinization, and the surface soil salinity showed strong variability. Specifically, the soil salinity of the plots showed a decreasing trend with increasing soil depth, and the variation degree was different. According to the correlation analysis, there was a significant correlation between the soil salinity, total root length, and specific root length (P < 0.01). Furthermore, the soil salinity was significantly correlated with the root/shoot ratio and root forks (P < 0.05), but not the root mean diameter. The P. australis specimens in the inland salt marshes showed the characteristics of sensitive plants. They adapted to the soil environment that had a strong salt variation by modifying their root morphology and changing the biomass allocation strategy. This phenomenon reflected the ecological adaptation mechanism used by wetland plants to cope with multiple environmental selection pressures under adverse stress conditions.