Fermentation of red grapefruit by Monascus purpureus (M. purpureus) results in complex changes in flavor compounds and metabolic profiles, but the specifics of these alterations are not well understood. This study aimed to investigate the changes in flavor compounds and metabolomic traits during this fermentation process. Using Headspace solid-phase microextraction-gas chromatography-mass spectrometry (HS-SPME-GC-MS) with non-targeted metabolomics, we analyzed flavor compounds and measured physicochemical indices throughout the fermentation period. We identified 23 volatile flavor metabolites before and after fermentation, focusing on acids, alcohols, and aldehydes, of these, 9 showed an upward effect and 14 showed a downward effect. Key metabolic pathways involved included butyric acid, taurine, and hypotaurine, with notable downregulation of acetone and 1-butanol in the butyric acid pathway. The study reveals that butyric acid-related metabolism influences other pathways such as glycolysis, fatty acid metabolism, and the tricarboxylic acid cycle in M. purpureus. These findings provide insights into the generation of flavor compounds during fermentation and offer a theoretical basis for the industrial production of fermented citrus fruits.