Soil salinity is rarely uniform, but the understanding of the physiological responses of plants to vertically heterogeneous salinity in the root zone is still limited. In the present study, pot experiments were conducted in a greenhouse from April to July in 2014 and 2015. In both experiments, four treatments, T-1:1, T-1:5, T-2:4 and T-3:3, differing in their vertical soil salt distributions, were established, with salt contents of 1 parts per thousand, 1 parts per thousand, 2 parts per thousand and 3 parts per thousand in the upper soil layer and 1 parts per thousand, 5 parts per thousand, 4 parts per thousand and 3 parts per thousand in the lower soil layer, respectively. Straw layer was buried to isolate the upper soil layer from the lower soil layer. The objectives of this research were to evaluate the effects of vertically heterogeneous salinity on the changes in the plant biomass, shoot Na+ and K+ contents, photosynthesis rate (P-n), stomatal conductance (g(s)), chlorophyll fluorescence and chlorophyll contents (Chl) of tomato plants (Solanum lycopersicum L.var. Yazhoufenwang). Under the similar average soil salt content, the heterogeneous salt distribution in the root zone (T-1.5) prevented Na+ accumulation and promoted K+ absorption compared with the homogeneous salt distribution (T-3.3) treatment, leading to an increase in the K+/Na+ ratio. The vertically heterogeneous soil salinity in both experiments was proved to benefit photosynthesis and the related physiological parameters in tomatoes, such as stomatal conductance (g(s)), maximum electron transport rate (ETRmax), maximal efficiency of PSII photo-chemistry (F-v/F-m), actual quantum yield of PSII (Phi(PSII)) and chlorophyll content (Chl). Significant increase was observed in these parameters in T-1:5 compared with T-3.3 during the fruiting and harvesting stages (P < 0.05). Chlorophyll fluorescence (ETRmax F-v/F-m and Phi(PSII) was found to be most closely related to the water-weighted mean soil salinity (P < 0.01) rather than to the lowest, highest or mean soil salinity in the root zone. The overall results suggested that vertically heterogeneous soil salinity could relieve salt stress and benefit photosynthesis and the related physiological parameters of tomato plants.