III-nitride-based two-dimensional photonic crystal (2D-PhC) cavities with high-quality factors (Q-factors) have a large potential application, however realized Q-factors in the visible wavelength regime have been relatively moderate. In this study, we demonstrate the design and fabrication of 2D-PhC cavities to achieve high Q-factors, especially in the visible range. From the comparison of numerical calculations and the experimental results, we discuss the dominant optical losses that limit the Q-factor of H3-type cavities formed in an Eu,O-codoped GaN film. Based on these results we designed 2D-PhC cavities which can effectively suppress these dominant losses. We fabricated 2D-heterostructures and show a high Q-factor of 10500 at a resonant wavelength of ∼660 nm, which is considerably larger than any existing GaN-based nano/micro-resonators in the visible region. This study provides design guidelines for the realization of high Q-factors in photonic crystal nanocavities based on III-nitride semiconductors.