A circuit carrier structure includes an inner circuit structure, at least one first circuit layer, and at least one heat dissipating structure. The inner circuit structure has a first surface and a second surface opposite to the first surface. The first circuit layer is disposed on the first surface of the inner circuit structure. The heat dissipating structure is disposed in the first circuit layer. The heat dissipating structure includes a first heat dissipating pattern, a second heat dissipating pattern and an interlayer metal layer. The first heat dissipating pattern is embedded in the corresponding first circuit layer. The second heat dissipating pattern is disposed on the first heat dissipating pattern. The interlayer metal layer is disposed between the first heat dissipating pattern and the second heat dissipating pattern. A manufacturing method of the circuit carrier structure is also provided.