Licorice, the dried roots and rhizomes of the Glycyrrhiza uralensis Fisch., holds a prominent status in various formulations within the realm of Chinese medicinal practices. The traditional processing methods of licorice hinder quality assurance, thus prompting Chinese medicine researchers to focus on the fresh processing methods to enhancing processing efficiency and quality. This study aimed to identify the differential compounds of licorice between traditional and fresh processing methods and provide a scientific basis for the fresh processing of licorice and for further research on the processing mechanism. A methodology integrating ultra-performance liquid chromatography with quadrupole-time-of-flight tandem mass spectrometry combined with multivariate statistical analysis was employed to characterize the differential compounds present in licorice between traditional processing and fresh processing. The results derived from principal component analysis and heat map analyses underscored significant differences in the content of bioactive compounds between the two processing methods. By applying conditions of VIP > 1.5 and p < 0.05, a total of 38 differential compounds were identified through t tests, and the transformation mechanisms of select compounds were illustrated. The adoption of fresh processing techniques not only improved processing efficiency but also significantly enhanced the preservation of bioactive compounds within licorice. This research has established a rapid and efficient analytical method for the identification of differential compounds present in differently processed licorice products.