We determine the topological susceptibility chi_t in the topologically-trivial sector generated by lattice simulations of N_f = 2+1 QCD with overlap Dirac fermion, on a 16^3 x 48 lattice with lattice spacing ~ 0.11 fm, for five sea quark masses m_q ranging from m_s/6 to m_s (where m_s is the physical strange quark mass). The chi_t is extracted from the plateau (at large time separation) of the 2-point and 4-point time-correlation functions of the flavor-singlet pseudoscalar meson eta, which arises from the finite size effect due to fixed topology. In the small m_q regime, our result of chi_t agrees with the chiral effective theory. Using the formula chi_t = Sigma(m_u^{-1} + m_d^{-1} + m_s^{-1})^{-1} by Leutwyler-Smilga, we obtain the chiral condensate Sigma^{MSbar}(2 GeV) = [249(4)(2) MeV]^3.