Phonon modes in shell quantum dots (SQDs) composed of a spherical AlAs core embedded in a GaAs shell, with up to about 12 000 atoms (about 8.5 nm in outer diameter), are calculated by using a valence force field model. All the vibration frequencies and amplitudes are evaluated directly from the lattice dynamic matrix by employing the projection operators of the group theory. The numerous SQD phonon modes in each of five symmetries which suffer more quantum confinement than modes in a usual quantum dot owing to the small scale of the shell's thickness are classified by using an analysis method both in real space and in reciprocal space. It is found that the bulk GaAs-like SQD modes with localization radius located in the interior of the shell have clearly pronounced bulk specific k-point parentage from a specific part of the Brillouin zone (BZ) (Γ derived, X derived etc) and from a definite bulk band (one of six modes). In AlAs/GaAs SQDs of all sizes, the bulk GaAs-LO(Γ)-like SQD modes always have A₁ symmetry, while the bulk GaAs-TO(Γ)-like and bulk-GaAs-A(Γ)-like dot modes have T₁ symmetry. The bulklike SQD mode of specific symmetry has a dominant BZ parentage peak around the bulk origins, so the frequencies of these SQD modes can be approximately related to a single bulk phonon band at a single wavevector k. In addition to the frequencies of bulk GaAs-A(Γ)-like SQD modes blue-shifting as the shell's characteristic scale reduces, the bulk-GaAs-like Γ-derived LO and TO SQD modes red-shift in frequency with decreasing shell characteristic scale. There is almost no LO/TO mixing for bulklike modes. The identification and classification of SQD modes have fundamental importance in the discussion of the Raman spectrum and electron–phonon interaction.