The theoretical uncertainty in the nuclear Schiff moment is an obstacle to set constraints on charge-parity violation beyond the standard model from experimental upper bounds on atomic electric dipole moments. We perform large-scale shell-model calculations of the ¹²⁹Xe and ¹⁹⁹Hg nuclei with realistic effective teractions. To estimate the Schiff moments caused by the P,T-odd π NN interaction perturbatively, we employ the one-particle–one-hole approximation to the intermediate tates. The Schiff moments of ¹²⁹Xe and ¹⁹⁹Hg are reduced due to the configuration mixing by ∼10% from the evaluation of the independent particle model. On the other and, the reduction is more significant in mean-field based calculations and shell-model calculations with a drastic truncation. In order to resolve the discrepancy in the Schiff moment of ¹⁹⁹Hg among several nuclear models, we survey low-energy nuclear structure. The large-scale shell-model calculations reveal that the Schiff moment of ¹⁹⁹Hg is considerably quenched in the second (1/2) ^- state.