Nanocolumn InGaN/GaN quantum-well crystals were deposited on pillared and flat Si substrates. A unique flower structure was synthesized on the Si pillars. Vertically aligned nanocolumn crystals were uniformly deposited on the flat Si substrate. Raman spectra measurement shows the crystals are fully relaxed. Photoluminescence measurement indicates much stronger photoluminescence excited from the flower structure than that from the crystals on the flat Si substrate. Reflectivity measurement demonstrates much lower reflectivity of the flower structure than that of the crystals on the flat substrate. Laser scanning confocal microscopy measurement indicates clear vertical photoluminescence distributions of the flower structure. Optical microscopy images show that there is a horizontal photoluminescence distribution on the pillared Si substrate and the quantum-well flower structure emits much brighter light than the crystals on the flat Si substrate. The flower structure improves the surface geometrical structure and enhances the extraction efficiency much more than the crystals on the flat Si substrate.