<p>Juan-Tong-Yin (JTY) is a clinically effective prescription for treating endometriosis (EM). However, its material basis and mechanisms of action are unclear. In this particular investigation, we used both metabolomics and network pharmacology to investigate the material basis and mechanisms underlying the therapeutic effects of JTY in the treatment of EM. In total, 37 blood entry compounds derived from JTY were identified by ultra-performance liquid chromatography-high resolution mass spectrometry technology (UPLC-MS/MS). The intersecting target genes of 101 genes associated with identified compounds in JTY and EM disease genes were identified using a network pharmacology approach. The protein interaction network revealed ESR1, ACTB, TP53, IL6, TNF, BCL2, and STAT3 as important targets. Gene Ontology (GO) analysis showed that negative regulation of apoptotic processes, cell proliferation, positive regulation of ERK1 and ERK2 cascade angiogenesis, positive regulation of I-kappaB kinase/NF-kappaB signaling, positive regulation of cell migration, and inflammatory response were the main functions, and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis showed that 20 pathways such as the sphingolipid signaling pathway and PI3K-Akt signaling pathway were the main pathways involved in the anti-EM effects of JTY. 39 potential metabolic markers and 7 possible metabolic pathways were identified by metabolomics analysis. Metabolomic analysis demonstrated that JTY's therapeutic efficacy could be attributed to the modulation of bile acid metabolism, phospholipid metabolism, phospholipid signaling pathways, unsaturated fatty acid biosynthesis. Combined network pharmacological and metabolomic analysis revealed that sphingolipid signaling psssway is a crossed metabolic pathway. Sphingosine-1-phosphate (S1P), sphingosine (Sph), Sphingomyelin (SM) are significantly enriched differential metabolite by the sphospholipid signaling pathway.</p>