The invention discloses a probing pad structure and a manufacturing method thereof. The probing pad structure is suitable to be arranged in a cutting street area of a wafer, is provided with a groove and a smaller sectional area, and provides a longer glide distance for a probe. The probing pad structure comprises a substrate, at least one conductive layer and at least one protective layer, wherein the substrate is provided with the groove; the conductive layer is arranged on the substrate; the conductive layer comprises a first metal layer and a second metal layer; the first metal layer is arranged on the groove; the second metal layer is arranged on the first metal layer, and extends to the substrate outside the groove; the protective layer is arranged on the conductive layer; the protective layer is provided with an opening; and the opening is arranged corresponding to the position of the groove.