Graphene moiré superlattices are outstanding platforms to study correlated electron physics and superconductivity with exceptional tunability. However, robust superconductivity has been measured only in magic-angle twisted bilayer graphene (MA-TBG) and magic-angle twisted trilayer graphene (MA-TTG). The absence of a superconducting phase in certain moiré flat bands raises a question on the superconducting mechanism. In this work, we investigate electronic structure and electron-phonon coupling in graphene moiré superlattices based on atomistic calculations. We show that electron-phonon coupling strength λ is dramatically different among graphene moiré flat bands. The total strength λ is very large (λ>1) for MA-TBG and MA-TTG, both of which display robust superconductivity in experiments. However, λ is an order of magnitude smaller in twisted double bilayer graphene (TDBG) and twisted monolayer-bilayer graphene (TMBG) where superconductivity is reportedly rather weak or absent. We find that the Bernal-stacked layers in TDBG and TMBG induce sublattice polarization in the flat-band states, suppressing intersublattice electron-phonon matrix elements. We also obtain the nonadiabatic superconducting transition temperature T_{c} that matches well with the experimental results. Our results clearly show a correlation between strong electron-phonon coupling and experimental observations of robust superconductivity.