Resonance effects caused by the photon–electron interaction are a focus of attention in semiconductor optoelectronics, as they are able to increase the efficiency of emission. GaN-on-silicon microdisks can provide a perfect cavity structure for such resonance to occur. Here we report GaN-based microdisks with different diameters, based on a standard blue LED wafer on a Si substrate. A confocal photoluminescence spectroscopy is performed to analyze the properties of all microdisks. Then, we systematically study the effects of radial modes and axial modes of these microdisks on photon–electron coupling efficiency by using three-dimensional finite-difference time-domain simulations. For thick microdisks, photon–electron coupling efficiency is found to greatly depend on the distributions of both the radial modes and the axial modes, and the inclined sidewalls make significant influences on the axial mode distributions. These results are important for realization of high-efficiency resonant emission in GaN-based microcavity devices.