Soil salinity is a major soil threat, causing severe environmental problems. Soil salt stress limits N uptake and cotton growth, especially in arid regions. However, the mechanism underlying stress tolerance in cotton plants under different soil salinity levels has not been fully elucidated. Therefore, the aim of this study was to examine the proportion and mechanism of cotton N uptake and transport under salt stress using the ¹⁵N isotope labeling technique. Cotton plants were grown in four undisturbed loamy soils (CK, non-salinity, 4.0 dS m⁻¹). The N transported to cotton from the 0–20 cm soil layer in C1 treatment was higher than from the 40–60 cm layer. Furthermore, the cotton fruit cultivated in C1 exhibited a notably elevated dry matter content compared to those cultivated in the control treatment. As the soil salt stress increased from the control treatment to C1, the cotton stems and fruits demonstrated a gradual enhancement in their N uptake and regulatory capabilities, albeit with a slight decrease observed in the leaves. These findings emphasize that soil salt stress diminishes cotton nitrogen uptake and transport, potentially exacerbating nitrogen pollution in the absence of optimized nitrogen fertilization.