The invention provides a circuit board structure and a manufacturing method thereof. The circuit board structure includes a line portion, a first insulating layer, and a conductive terminal. The first insulating layer is disposed on the line portion. The conductive terminal is disposed on the first insulating layer and embedded in the first insulating layer to be electrically connected with the line portion. The conductive terminal includes a first portion, a second portion, and a third portion. The first portion protrudes from a surface of the first insulating layer. The second portion is embedded in the first insulating layer and connected to the first portion. The third portion is disposed between the line portion and the second portion. A width of the second portion is greater than a width of the third portion.