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Abstract Background The plant Alisma plantago-aquatica Linnaeus, which is widely distributed in southwest of China, is the main material of traditional Chinese medicine “Zexie”. It was used as folk medicine for immune-modulation, anti-tumor, anti-inflammatory and antibacterial. Previous chemical studies on A. plantago-aquatica reported the identification of triterpenes, diterpenes, sesquiterpenes, steroids, alkaloids and phenolic acid. Terpenes and phenolic acid were regard as major secondary metabolites from this medicine plant. Results A new phenolic acid, plantain A (1), along with four known compounds (2–5) were isolated and identified from A. plantago-aquatica by extensive chromatographic and spectrometric methods. In the present study, the levels of TNF-α, IL-1β, COX-2, PEG2 and TGF-β1 were increased in model group rats, whereas on treatment with the isolated compound (1 and 4) at 50 mg/kg, there was a significant decrease in the cytokine levels. Therefore, the anti-CNP effect of 1 and 4 may be related to their anti-inflammatory properties. Conclusions A new phenolic acid and four known phenolic compounds were isolated from A. plantago-aquatica. Moreover, compounds 1 and 4 shows significant anti-chronic prostatitis activity in rats.