We employ an optical pump-probe technique to study coherent phonon oscillations in Ca2RuO4. We find that oscillation amplitude of an Ag symmetric phonon mode is strongly suppressed at 260 K, a putative transition point of orbital ordering. The oscillation also shows a gradual but huge change in its phase, such that the oscillation even flips over with a 180 change across the temperature. Density functional theory calculations indicate that the Ag phonon has an eigenmode of octahedral distortion with conventional tilting along the a axis and antipolar distortion of apical oxygen. Careful inspection of the lattice captures an unusually large antipolar distortion in low-temperature structures, which may play a crucial role for the phase transition at 260 K.