We study the radiative heat transfer between multilayer structures made by a periodic repetition of a graphene sheet and a hexagonal boron nitride (hBN) slab. Surface plasmons in a monolayer graphene can couple with hyperbolic phonon polaritons in a single hBN film to form hybrid polaritons that can assist photon tunneling. For periodic multilayer graphene/hBN structures, the stacked metallic/dielectric array can give rise to a further effective hyperbolic behavior, in addition to the intrinsic natural hyperbolic behavior of hBN. The effective hyperbolicity can en- able more hyperbolic polaritons that enhance the photon tunneling and hence the near-field heat transfer. However, the hybrid polaritons on the surface, i.e., surface plasmon-phonon polaritons, dominate the near-field heat transfer between multilayer structures when the topmost layer is graphene. The effective hyperbolic regions can be well predicted by the effective medium theory (EMT), thought EMT fails to capture the hybrid surface polaritons and results in a heat trans- fer rate much lower compared to the exact calculation. The chemical potential of the graphene sheets can be tuned through electrical gating and results in an additional modulation of the heat transfer. We found that the near-field heat transfer between multilayer structures does not increase monotonously with the number of layers in the stack, which provides a way to control the heat transfer rate by the number of graphene layers in the multilayer structure. The results may benefit the applications of near-field energy harvesting and radiative cooling based on hybrid polaritons in two-dimensional materials.