We study the superfluid phases of a Fermi gas in a multilayer optical lattice system in the presence of out-of-plane Zeeman field, as well as spin-orbit (SO) coupling. We show that the Zeeman field combined with the SO coupling leads to exotic topological pair-density wave (PDW) phases in which different layers possess different superfluid order parameters, even though each layer experiences the same Zeeman field and the SO coupling. We elucidate the mechanism of the emerging PDW phases, and characterize their topological properties by calculating the associated Chern numbers.