We design and fabricate ultra-high-quality (Q) photonic nanocavities in a symmetrically glass-clad silicon (Si) two-dimensional (2D) photonic crystal (PhC) structure. We theoretically investigate the dependence of the refractive index of the glass on the Q factors for asymmetric and symmetric structures. We show that the index-symmetric distribution of the glass is a critical factor to realize ultrahigh Q factors for glass-clad 2D PhC structures. We fabricate symmetrically glass-clad Si PhC nanocavities and achieve a record Q factor of 1×10(6), comparable with the highest Q factors of nanocavities in air-bridge structures.