An inner-layer heat-dissipating board and a multi-chip stack package structure having the inner-layer heat-dissipating board are disclosed. The inner-layer heat-dissipating board includes a metal board body formed with a plurality of penetrating conductive through holes each comprising a plurality of nano wires and an oxidative block having nano apertures filled with the nano wires. The multi-chip stack package structure includes a first chip and an electronic component respectively disposed on the inner-layer heat-dissipating board to thereby facilitate heat dissipation in the multi-chip stack structure as well as increase the overall package rigidity.