The invention discloses a SiO<2> channel type chalcogenide waveguide with protective layer and a preparation method thereof, and solves the problem of rough channel side wall roughness in preparationof the SiO<2> channel type waveguide in the prior art, the key point of the technical scheme is that coating a photoresist as a mask layer on the surface layer of SiO<2> of the Si/SiO<2> substrate, and the Si/SiO<2> substrate with the mask layer is put into an ICP etching machine to etch the SiO<2> channel, adjusting etching precision by introducing an argon gas and a trifluoromethane gas, and sequentially plating an As2Se3 chalcogenide thin film and a SU-8 polymer on the Si/SiO<2> substrate with the SiO<2> channel, finally stripping the mask layer and the As2Se3 chalcogenide thin film and theSU-8 polymer on the mask layer from the Si/SiO<2> substrate to obtain a waveguide. According to the SiO<2> channel type chalcogenide waveguide with the protective layer and the preparation method thereof, the etching parameters are optimized by controlling the ratio of the argon gas and the trifluoromethane gas, so that minimizing the roughness of the side wall of the SiO<2> channel, and reducingthe roughness of the side wall of the waveguide.