Bilayer honeycomb lattice, with inter-layer tunneling energy, has a parabolic dispersion relation, and the inter-layer hopping can cause the charge imbalance between two sublattices.Here, we investigate the metal-insulator phase transitions on the strongly correlated bilayer honeycomb lattice by cellular dynamical mean-field theory combined with continuous time quantum Monte Carlo method.We have studied the density of states, spectral function near Fermi surface and double occupancy to determine the boundary of metal-insulator phase transition.Then, we investigate the magnetic phase transition.We find that the procedures of magnetic spontaneous symmetry breaking on dimer and non-dimer sites are different, causing a novel phase transition between normal anti-ferromagnet and layer anti-ferromagnet.The whole phase diagrams about the magnetism, temperature, interaction and inter-layer hopping are obtained.