Plant growth in the heterogeneous salinity soil is better than that of in the uniform salinity soil, thus, planting salt tolerant plants in the partial zone desalinated soil of the saline land may reduce the revegetation costs. The swamp rose mallow (Hibiscus moscheutos, SRM), which is an important landscape plant that grows in coastal saline lands, may be an optional plant that can adapt to the non-uniform salinity soil. In this study, SRM seedlings grown in split-root pots irrigated with different concentration of NaCl solutions were studied. There were four treatments, a control (0 mM NaCl), uniform salinity (200 mM NaCl), and two non-uniform salinities (0/200 mM and 0/400 mM NaCl). We determined the growth, gas exchange properties of the leaves, morphological parameters of the leaves and roots, water potential and consumption, and ion accumulation of the seedlings. The aim was to reveal the physiological and anatomical responses of SRM to non-uniform salinity. Under non-uniform salinity, the total biomass, shoot height, and leaf area of SRM seedlings were significantly higher and the leaf Na+ and Cl− contents were significantly lower than under uniform salinity. The total biomass was negatively corelated with the mean root zone salinity. Once the parts of the roots were in the salt-free zone, the leaf water potential and the daily water consumption of the seedlings under non-uniform salinity were much higher than the uniform salinity treatment. The leaf gas exchange of SRM under non-uniform salinity was not significantly inhibited compared to the control, but was significantly higher than under uniform salinity. The leaf electron transport rate (ETR) and maximum quantum yield (Fv/Fm) of the PSII, leaf SOD activity, and the MDA content of the seedlings subjected to non-uniform salinity treatments were at unstressed level. In terms of leaf anatomical traits, that the palisade and spongy parenchyma was significantly thicker than the uniform salinity. Early senescence of the leaves was observed under both uniform and non-uniform salinity conditions. More roots, especially fine roots, were distributed in the non-saline zone. These results indicate that under non-uniform salinity, SRM seedling growth was significantly inhibited, however, the salt stress was alleviated by the partial salt-free root zone compared to uniform the salinity. Non-uniform salinity led to moderate Na+ accumulation in the leaves, which in turn caused slight oxidative and osmotic stress, but had little influence on the morphological or anatomical traits of the leaves. SRM could adapt to the saline soil where partial zone desalinated or partial zone replaced by the non-saline soil.