Soil salinization is one of the main factors affecting soil use efficiency in China. Phragmites australis is a good experimental material for improving soil salinization. Phragmites australis has a variety of ecotypes, and determination of salt tolerance differences among ecotypes of Phragmites australis is an urgent problem to be solved. By setting up freshwater and saltwater treatments, and measuring the growth index and photosynthetic index of Phragmites australis in both, an experiment was conducted to compare the salinity of estuarine reeds and landlocked reeds, and to find biological material to combat soil salinization. Compared with the freshwater treatment, the height and transpiration rate (E) of landlocked reeds significantly decreased under the condition of salt addition, but the water use efficiency (WUE) of both ecotypes significantly increased. The relative growth rate (RGR) and stomatal conductance (Gs) of estuarine reeds were significantly higher than those of inland reeds. In the freshwater environment, the relative growth rate (RGR) and net photosynthetic rate (A) of estuarine reeds were significantly higher than those of inland reeds. The results showed that there was a certain degree of differentiation between the two ecotypes of reeds during the evolutionary process and that salt stress inhibited the growth of both ecotypes. The relative growth rate (RGR) and stomatal conductance (Gs) of the two ecotypes of reed showed significant differences under salt stress, which indicates that the responses of the two ecotypes to salinity are different. In comparison to inland reeds, estuarine reeds are more resistant to salt stress. The differences in phenotypic traits of inland and estuarine reeds are mainly determined by the differences in their in situ habitats.