C-based XC binary materials and their (XC)m/(YC)n (X, Y ≡ Si, Ge and Sn) superlattices (SLs) have recently gained considerable interest as valuable alternatives to Si for designing and/or exploiting nanostructured electronic devices (NEDs) in the growing high-power application needs. In commercial NEDs, heat dissipation and thermal management have been and still are crucial issues. The concept of phonon engineering is important for manipulating thermal transport in low-dimensional heterostructures to study their lattice dynamical features. By adopting a realistic rigid-ion-model, we reported results of phonon dispersions ωjSLk→ of novel short-period XCm/(YC)n001 SLs, for m, n = 2, 3, 4 by varying phonon wavevectors k→SL along the growth k|| ([001]), and in-plane k⟂ ([100], [010]) directions. The SL phonon dispersions displayed flattening of modes, especially at high-symmetry critical points Γ, Z and M. Miniband formation and anti-crossings in ωjSLk→ lead to the reduction in phonon conductivity κz along the growth direction by an order of magnitude relative to the bulk materials. Due to zone-folding effects, the in-plane phonons in SLs exhibited a strong mixture of XC-like and YC-like low-energy ωTA, ωLA modes with the emergence of stop bands at certain k→SL. For thermal transport applications, the results demonstrate modifications in thermal conductivities via changes in group velocities, specific heat, and density of states.