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Fructus Aurantii (FA) is an edible and medicinal functional food used worldwide that enhances digestion. Since raw FA (RFA) possesses certain side effects for some patients, processed FA (PFA) is commonly used in clinical practice. This study aimed to establish an objective and comprehensive quality evaluation of the PFA that employed the technique of steaming and fermentation. Combined with the volatile and non‐volatile components, as well as the regulation of gut microbiota, the differentiation between RFA and PFA was analyzed. The results showed that the PFA considerably reduced the contents of flavonoid glycosides while increasing hesperidin‐7‐O‐glucoside and flavonoid aglycones. The electronic nose and GC‐MS (Gas chromatography/mass spectrometry) effectively detected the variation in flavor between RFA and PFA. Correlation analysis revealed that eight volatile components (relative odor activity value [ROAV] ≥ 0.1) played a key role in inducing odor modifications. The original floral and woody notes were subdued due to decreased levels of linalool, sabinene, α‐terpineol, and terpinen‐4‐ol. After processing, more delightful flavors such as lemon and fruity aromas were acquired. Furthermore, gut microbiota analysis indicated a significant increase in beneficial microbial taxa. Particularly, Lactobacillus, Akkermansia, and Blautia exhibited higher abundance following PFA treatment. Conversely, a lower presence of pathogenic bacteria, including Proteobacteria, Flexispira, and Clostridium. This strategy contributes to a comprehensive analysis technique for the quality assessment of FA, providing scientific justifications for processing FA into high‐value products with enhanced health benefits. Practical Application: This study provided an efficient approach to Fructus Aurantii quality evaluation. The methods of fermentation and steaming showed improved quality and safety. [ABSTRACT FROM AUTHOR]