A manufacturing process of a high thermal conducting circuit substrate is provided. First, a metal core substrate is provided and then the metal core substrate is etched at different etching speeds. Afterwards, two insulating layers are formed respectively on two sides of the etched metal core substrate. In addition, as an option, two conducting layers are formed respectively on two sides of the metal core substrate and are on top of the insulting layers. The conducting layers are patterned according to designs appropriate for the products. Because the high thermal conducting circuit substrate fabricated as the aforementioned manufacturing process mainly comprises the metal core substrate, it helps to elevate the thermal conduction of the circuit substrate itself.