We demonstrate that the mean structures of molecules derived from quasiclassical direct ab initio molecular dynamics (MD) simulation, the classical simulation that takes into account quantum vibrational levels, agree well with those determined horn quantum-mechanical (QM) expectation values and/or experimentally observed values. First, for a one-dimensional model potential that includes anharmonicity as the third-order potential energy term, we show that the time-averaged structure over the classical trajectory with taking account of a quantum vibrational energy level correlates with a QM structure averaged using a vibrational wave function based on the first-order perturbation theory. Next, quasiclassical direct ab initio MD and Fourier grid Hamiltonian method are applied to OH and OD radicals; the mean structures at several vibrational levels of both classical and QM methods coincide, and they are in good agreement with the structures determined experimentally. Quasiclassical direct ab initio MD is then applied to H2O, C2H2, and C6H6. For H2O and C2H2, the classical mechanically calculated mean structural parameters agree well with the experimental values, and the QM values obtained from vibrational self-consistent field. For C2H2, we find that r(g)(C-H) is longer than r(e)(C-H), whereas r(mean)((0))(C-H), which is equal to r(t)(C-H), is slightly shorter than r(e)(C-H).