An optical waveguide structure and a manufacturing method thereof are provided. The optical waveguide structure includes: a substrate; a first-type semiconductor conductive layer disposed on the substrate; a first confining layer disposed on the first-type semiconductor conductive layer; a waveguide layer disposed on the first confining layer and including a luminescent material; a polymer filling layer disposed on the first confining layer and adjacent to the waveguide layer, wherein the viscosity of the polymer filling layer is less than 52 mm2/s; a second confining layer disposed on the waveguide layer and the polymer filling layer; a cladding layer disposed on the second confining layer; and a second-type semiconductor conductive layer disposed on the cladding layer.