Abstract Here we present a detailed study on nitridation and structure transition in monoclinic gallium oxide (β-Ga2O3) nanowires grown on Si substrates with chemical vapor phase epitaxy. The nanowires were systematically nitridated at different temperatures. Their morphologies and microstructures were precisely characterized using field-emission scanning electron microscopy (SEM), high-resolution transmission electron microscopy (HRTEM), and confocal micro-Raman spectroscopy. It is found that heat treatment of Ga2O3 nanowires in the gas of ammonia results in rich substructures including the Ga2O3 phase, the crystalline GaN phase, and other meta structures. The identification of these structures helps to understand some interesting phenomena observed in nanostructures, such as the microstructural origin of the unknown Raman lines in GaN nanowires.