We investigate the improvement of the conversion efficiency of ultra-thin (~500nm-thick) microcrystalline silicon (μc-Si) solar cells incorporating photonic-crystal structures, where light absorption is strongly enhanced by the multiple resonant modes in the photonic crystal. We focus on the quality of the intrinsic μc-Si layer deposited on the substrate, which is structured to form a photonic crystal at its upper surface with a period of several hundred nanometers. We first study the crystalline quality from the viewpoint of the crystalline fraction and show that the efficiency can be improved when the deposition conditions for the μc-Si layer are tuned to give an almost constant crystalline fraction of ~50% across the entire film. We then study the influence of the photonic-crystal structure on the crystalline quality. From transmission-electron microscope images, we show that the collision of μc-Si grains growing at different angles occurs when a photonic-crystal structure with an angular surface is used; this can be suppressed by introducing a rounded surface structure. As a result, we demonstrate an efficiency of 8.7% in a ~500-nm thick, homo-junction μc-Si solar cell, which has only ~1/4 the thickness of typical μc-Si solar cells. We also discuss the possibility of further improving the efficiency by performing calculations that focus on the absorption characteristics of the fabricated cell structure.