Background: Previous research has demonstrated that Herba Lysimachiae (HL) exerts the dual effects on platelet aggregation in the synovium, which may contribute to its protection against synovial lesions under different situations. However, the mechanism is unclear. In the present experiment, a biolabel research based on metabonomics was used to mine more information about the intervention of HL on synovium at the metabolite level, which may help to analyze the regulation of HL on synovial platelet aggregation and its possible treatment in synovial diseases. Methods: Synovial metabolic profiling was analyzed using a Shimadzu Nexera UHPLC LC-30A system and an AB SCIEX Triple TOF 4600 mass spectrometer. Enzyme-linked immunosorbent assay was used to verify the biolabels analysis results. Results: Totally, thirteen common metabolites were differentially expressed after treating with HL, and implicated in 2 key pathways (arachidonic acid metabolism and glycerophospholipid metabolism). ELISA showed that HL up-regulated the expression of prostaglandins E1 and E2 in synovial tissues. Conclusions: This study reveals that HL may regulate the synovial platelet aggregation through prostaglandin E1/E2. Additionally, HL is suitable for treating synovial diseases, especially osteoarthritis, which may be associated with the platelet aggregation, apoptosis, inflammation, angiogenesis, and carcinogenesis processes.