Disclosed are a flip-chip bonding structure for improving the vertical alignment of an optical device relative to a PLC and a flip-chip bonding method for achieving this structure. The flip-chip bonding structure includes: a semiconductor substrate; a lower-clad layer formed on the upper surface of the semiconductor substrate, wherein the lower-clad layer is depressed on a designated area for mounting an optical device; vertical alignment structures formed on a part of the upper surface of the depressed area of the lower-clad layer and determining a vertical alignment position of the optical device on the semiconductor substrate; electrodes formed on another part of the upper surface of the depressed area of the lower-clad layer; a solder bump formed on the upper surfaces of the electrodes; and, an optical device bonded to the substrate by a flip-chip bonding method using the solder bump.