Study on the relative contributions of phenotypic plasticity and genetic variation to plant phenotypic differentiation can facilitate the predictions of community composition and ecosystem functioning under global environmental changes. As a cosmopolitan grass, common reed (Phragmites australis) has a high intraspecific diversity and has several ecotypes in northwest and east China. However, few studies focused on the phenotypic variation of common reed at a larger scale in China. Here, we investigated the intraspecific variation in plant functional traits of P. australis from Ningxia Plain, an upstream wetland, and the Yellow River Delta, a downstream wetland, via field investigation and common garden experiment. The results showed that the shoot diameter, leaf length and leaf width of P. australis from the Yellow River Delta were significantly larger than those from the Ningxia Plain in both the field and the common garden, suggesting a stable phenotypic differentiation controlled by genetic variation between the two regions. The phenotypic differentiation could be explained by the adaptation to local climatic conditions such as precipitation. In the field, the shoot height and the leaf thickness of P. australis from Ningxia Plain were significantly higher than those from the Yellow River Delta, but the difference disappeared or reversed in the common garden, which suggests that these traits are regulated directly by the current environment and phenotypic plasticity is also an important mechanism for P. australis to adapt to environmental changes. In the common garden, the content of nitrogen and phosphorus in leaves of P. australis from Ningxia Plain was lower, while the plant density was significantly larger than that from the Yellow River Delta. Which reflects different adaptive strategies that P. australis from Ningxia Plain prefers a ruderal strategy with a high reproduction rate, while P. australis from the Yellow River Delta favors a competitive strategy. Moreover, there were correlations between the field and the common garden observations in shoot height, leaf length and relationship between shoot diameter and specific leaf area, which indicates the genetic inheritance of trait variation and trade-off strategy. In conclusion, there is an adaptive differentiation between the upstream and downstream populations of P. australis in the Yellow River basin due to phenotypic plasticity and genetic variation. Further studies are needed to reveal the responses of plant from different provenances to future changes of the multiple environmental factors.