We compute the topological susceptibility $chi_t$ of 2+1-flavor lattice QCD with dynamical Mobius domain-wall fermions, whose residual mass is kept at 1 MeV or smaller. In our analysis, we focus on the fluctuation of the topological charge density in a slab sub-volume of the simulated lattice, as proposed by Bietenholz et al. The quark mass dependence of our results agrees well with the prediction of the chiral perturbation theory, from which the chiral condensate is extracted. Combining the results for the pion mass $M_pi$ and decay constant $F_pi$, we obtain $chi_t$ = 0.227(02)(11)$M_pi^2 F_pi^2$ at the physical point, where the first error is statistical and the second is systematic.