Bee pollen and its extracts have been used for decades as therapeutic agents or health food supplements to alleviate chronic nonbacterial prostatitis (CNP). However, the functional compounds in bee pollen that are anti‐CNP remain still unclear. In this study, we evaluated the anti‐CNP properties of six principal phenolamides in bee pollen. Our results provide compelling evidence that the anti‐CNP property of bee pollen may be ascribed to its abundance of phenolamides. Particularly, di‐ p ‐Coumaroyl spermidine can alleviate CNP by upregulating autophagy via the AMPK/mTOR signaling pathway and regulating gut microbiota, based on the cellular and rat models. Additionally, our finding may provide a novel insight into the gut–prostate axis by regulating di‐ p ‐Coumaroyl spermidine. This is the first report that di‐ p ‐Coumaroyl spermidine in bee pollen possesses the anti‐prostatitis function. This paper will likely be helpful further to develop functional foods, personalized nutraceuticals, and medicine from bee pollen.