The invention discloses an optical fiber and silicon waveguide coupling structure based on polymer waveguides and a manufacturing method of the optical fiber and silicon waveguide coupling structure. The optical fiber and silicon waveguide coupling structure based on the polymer waveguides comprises an SOI wafer and an optical fiber arranged on the SOI wafer, the polymer straight waveguide and the polymer tapered waveguide are arranged on a buried oxide layer of the SOI wafer in sequence from right to left, the narrower end of the polymer tapered waveguide is connected with the polymer straight waveguide, and the wider end of the polymer tapered waveguide is aligned with a fiber core of the optical fiber; the silicon waveguide is arranged on upper layer silicon, the left end of the silicon waveguide is a back taper structure with a gradually changing width, the right end of the silicon waveguide is of a straight silicon waveguide back taper structure, part of the straight silicon waveguide wrapped in the polymer straight waveguide, and other parts of the straight silicon waveguide is covered with a silicon dioxide covering layer; a V-shaped groove is formed in the top surface of the left end of the SOI wafer, the silicon dioxide covering layer, the upper layer silicon and the buried oxide layer sequentially penetrate through the V-shaped groove in the depth direction, and the bottom end of the V-shaped groove is located at substrate silicon; the optical fiber is fixed in the V-shaped groove. The optical fiber and silicon waveguide coupling structure based on the polymer waveguides and the manufacturing method of the optical fiber and silicon waveguide coupling structure not only improve coupling efficiency, reduce process complexity and guarantee the reliability of the optical fiber coupling structure.