Abstract: Natural products are effective in the treatment and the prevention of human, animal and plant diseases. Therefore, natural products may also be considered to treat fish diseases. Acori Tatarinowii Rhizoma (ATR) is a herbal medicine with anti-inflammatory and antioxidant effects. However, little is known about how its active ingredients exert the beneficial effects. Here, Four effective active ingredients of ATR and their 81 targets were investigated, which affected the anti-inflammatory response. Among them, kaempferol-JUN was identified as a key regulatory module in anti-inflammatory immune responses, and kaempferol interacted with the CiJUN protein and inhibited CiJUN levels. Silencing CiJUN gene in Ctenopharyngodon idella kidney (CIK) cells enhanced anti-inflammatory activity and resistance to Aeromonas hydrophila, whereas anti-inflammatory activity and resistance were impaired after CiJUN overexpression. The mortality rate of diseased grass carp was reduced after treatment with kaempferol, as were the inflammatory and oxidant effects. Also, grass carp showed enhanced anti-inflammatory and antioxidant effects after feeding with kaempferol. The results provide further insights into the use of kaempferol to prevent and treat fish diseases.