Objective To investigate the effect of processing methods on Polygonatum kingianum Collett & Hemsl. metabolites, to reveal the regulatory pattern of processing methods on the metabolites, and to clarify the characteristic metabolites enriched by various processing methods.Methods Metabolites of P. kingianum samples processed via boiling (BP), roller processing (HP), and traditional processing (JZ) are analyzed using ultra-high performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS) based on widely targeted metabolomics. Differential metabolites are screened using multivariate statistical analyses, including principal component analysis, orthogonal partial least squares-discriminant analysis, and hierarchical clustering analysis, followed by Kyoto Encyclopedia of Genes and Genomes (KEGG) metabolic enrichment analysis.Results A total of 841 metabolites are detected in the P. kingianum samples processed by three methods, among which 438 core differential metabolites are identified, mainly belonging to eight classes, including alkaloids, flavonoids, phenolic acids, and steroids. Hierarchical clustering heatmap analysis reveals a significant separation among the groups and clustering within each group, indicating significant metabolic differences. Specifically, flavonoids are preferentially enriched in the BP group, with rutin and phloretin showing the highest relative abundances. Alkaloids reach the highest abundance in the JZ group, with a high relative content of ephedrine. According to KEGG enrichment analysis, the differential metabolites are mainly annotated and enriched in flavonoid biosynthesis, flavone and flavonol biosynthesis, as well as tryptophan and tyrosine metabolism pathways.Conclusion Different processing methods can significantly change the composition and content of P. kingianum Collett & Hemsl. metabolites. BP specifically enriches flavonoids, whereas JZ specifically enriches alkaloids. Furthermore, flavonoid biosynthesis and its derivative pathways are the core metabolic pathways that differentiate these processing methods.