The invention discloses a silicon dioxide optical waveguide device based on a B-Ge-codoped upper cladding and a preparation method thereof. The preparation method comprises the following steps of: sedimentating a silicon dioxide lower cladding on a substrate, sedimentating a Ge-doped silicon dioxide film on the upper surface of the lower cladding, forming waveguide sandwich layers with a square cross section by lithography and etching processes; sedimentating a B-Ge-codoped silicon dioxide upper cladding on the silicon dioxide lower cladding and the waveguide sandwich layers without forming agap between the upper cladding and the waveguide structure of the sandwich layer; and carrying out a high-temperature thermal-annealing process on the sedimented B-Ge-codoped silicon dioxide upper cladding and refluxing the upper cladding film with a low melting point into a gap between adjacent waveguide sandwich layers so that the shadowing effect action is lessened in a subsequent sedimentation film layer to fully fill the inter-waveguide gap and lessen the device loss. The silicon dioxide waveguide device structure based on the B-Ge-codoped upper cladding can be widely applied to devices in a waveguide structure with a high aspect ratio, such as splitters, couplers, array waveguide gratings, and the like.