Soil salinity influences plant growth and crop yield significantly. Former studies indicated that uneven salt distribution in the root zone could relieve salt stress. But, how uneven salt distribution influences Na+ and Ca2+ concentration in the stem, leaf, and fruit and whether this influence would bring effects on fruit blossom-end rot (BER) still needs to be further studied. Under consideration of this, pot experiment with four treatments, T1:1, T1:5, T2:4, and T3:3, was conducted by setting the upper soil layer salinity at 1‰, 1‰, 2‰, and 3‰ and the lower soil layer at salinities of 1‰, 5‰, 4‰, and 3‰, respectively. Compared with the uniform salt concentration in the root zone (T3:3 treatment), the incidence of BER in the T1:5 and T2:4 treatments decreased by 60% and 35%, respectively. The fruit Na+ concentration and Na+/Ca2+ ratio were positively correlated with the incidence of BER. The value of the upper-root selective absorption Ca2+ over Na+ (SCa/Na(upper root)) for T1:5 was 0.8 times more than that of T1:1. The results showed that the incidence of BER was positively correlated with root dry matter and SCa/Na(root) weighted mean salinity. The overall results suggested that uneven salt distribution in the root zone could promote the Ca2+ absorption, Ca2+/Na+ ratio, and selective absorption Ca2+ over Na+ and consequently decrease the incidence of BER in tomato fruit.