The invention discloses an embedded type circuit structure and a manufacturing method thereof. The manufacturing method comprises the following steps: firstly, providing a circuit board which is provided with a core layer and two embedded circuits embedded in two opposite surfaces of the core layer respectively; secondly, forming a conductive channel running through the circuit board, and two conductive layers which are electrically connected with the conductive channel and are coated on and electrically connected with the two embedded circuits respectively; thirdly, forming two resistance clad layers on the two conductive layers respectively, wherein each resistance clad layer is provided with a first opening to expose the surfaces of the conductive layers; fourthly, forming an anti-oxidation layer on the surface of each conductive layer; fifthly, removing the two resistance clad layers and the two conductive layers to expose the two embedded circuits; and finally, forming two anti-welding layers to cover the two embedded circuits respectively, wherein each anti-welding layer is provided with a second opening to expose the anti-oxidation layer.