An optical waveguide structure and a manufacturing method thereof are disclosed. The optical waveguide structure has a first waveguide layer, a binding layer, and a second waveguide layer. The first waveguide layer has a taper portion, a connecting portion, and a strip portion. The manufacturing method of the optical waveguide structure has steps of etching to form the first waveguide layer, and then etching to form the second waveguide layer under the first waveguide layer.