Soil salinity typically exhibits non-uniform distribution in the natural environment. However, how vertically non-uniform distribution of soil salinity in the root zone (VNDSR) regulated plant nitrogen metabolism is still largely elusive. This study aimed to investigate the impact of VNDSR on leaf Malondialdehyde (MDA) content, upper and lower root activity, leaf Na+/Ca2+ and Na+/K+, various tomato organs’ nitrogen concentration (%) and natural abundance of nitrogen isotopes (δ15N,‰), and nitrogen utilization efficiency of tomato plants. Four treatments were established, including the upper layer of the root zone having soil salinity levels of 1 ‰, 1 ‰, 2 ‰, and 3 ‰, while the corresponding lower layer of the root zone had soil salinity levels of 1 ‰, 5 ‰, 4 ‰, and 3 ‰, respectively, denoted as T1:1, T1:5, T2:4, and T3:3. The results showed that under the same average soil salinity conditions and compared to the treatment with uniform soil salinity distribution in the root zone (T3:3), the VNDSR treatment (T1:5) significantly reduced leaf MDA content (p < 0.01), Na+/Ca2+ (p < 0.01) and Na+/K+ (p < 0.01), and stem δ15N values (p < 0.05). Moreover, the VNDSR treatment (T1:5) significantly increased the ratio of upper and lower root biomass-weighted root activity (p < 0.01), tomato fruit yield (p < 0.01), and nitrogen partial factor productivity (PFP, gg−1, p < 0.01) compared to uniform salt distribution treatment (T3:3). There were significant positive correlations (p < 0.05) between leaf δ15N values and Nitrogen Absorption Ratio (NAR, %, p < 0.05) and PFP (p < 0.05), indicating that under VNDSR, δ15N values can serve as an indicator that comprehensively reflects the information of plant nitrogen utilization efficiency. In conclusion, the VNDSR could mitigate the damage of salt stress to tomatoes, enhance plant nitrogen uptake and utilization efficiency, and promote the growth and development of tomatoes. Data AvailabilityThe datasets generated or analyzed during the current study are available from the corresponding author on reasonable request.