We theoretically investigated the chiral phonons of honeycomb-type bilayer Wigner crystals recently discovered in van der Waals structures of layered transition metal dichalcogenides. These chiral phonons can emerge under the inversion symmetry breaking introduced by an effective mass imbalance between the two layers or a moiré potential in one layer, as well as under the time-reversal symmetry breaking realized by applying a magnetic field. Considering the wide tunability of layered materials, the frequencies and chirality values of phonons can both be tuned by varying the system parameters. These findings suggest that bilayer honeycomb-type Wigner crystals can serve as an exciting new platform for studying chiral phonons.