Judicious design of acoustic metamaterials has so far permitted control of topologically-protected waves in one plane of a two-dimensional system. Here, the symmetry of a phononic crystal is tuned geometrically to realise independent tuning of both in-plane and out-of-plane topological modes in the same frequency range. Valley degree of freedom, associated with the valley topological phase, has propelled the advancement of the elastic waveguide by offering immunity to backscattering against bending and weak perturbations. Despite many attempts to manipulate the wave path and working frequency of the waveguide, internal characteristic of an elastic wave such as rich polarization has not yet been utilized with valley topological phases. Here, we introduce the rich polarization into the valley degree of freedom, to achieve topologically protected in-plane and out-of-plane mode separation of an elastic wave. Accidental degeneracy proves its real worth of decoupling the in-plane and out-of-plane polarized valley Hall phases. We further demonstrate independent and simultaneous control of in-plane and out-of-plane waves, with intact topological protection. The presenting procedure for designing the topologically protected wave separation based on accidental degeneracy will widen the valley topological physics in view of both generation mechanism and application areas.