The invention relates to the laser field, in particular to a waveguide structured frequency doubler and a manufacturing method thereof. The invention utilizes multiple optical processing, cutting, polishing to manufacture a frequency doubling crystal wafer (or a crystal wafer bonded with a substrate), employs gluing, deepened optical cementing processes to bond the frequency doubling crystal wafer ( or the crystal wafer bonded with the substrate )to the substrate, and then process and polishes the frequency doubling wafer ( or the crystal wafer boned with the substrate ) on the substrate into required dimension of the waveguide structure. The lateral side of the frequency doubling crystal wafer is coated by a low refractive index deepened optical cement layer or glue layer, thereby forming the waveguide structured frequency doubler, wherein the utilized crystal can generate frequency doubling or multiple harmonic wave via critical phase matching, or can generate frequency doubling or higher harmonic wave via non-critical phase matching. The invention overcomes defects of the conventional doublers, and enables optical power density to be much larger than power density of light beams, thereby easily realizing non-linear effect of waveguide materials and further greatly increasing efficiency of the non-linear effect thereof.