Chronic nonbacterial prostatitis (CNP) is a common urology disease. Our previous research found Poria cocos polysaccharides (PPs) alleviated CNP and suggested the effect was related to gut bacteria. We investigated the crucial bacteria and their metabolites responsible for the anti-CNP effect to discover possible mechanisms. The results showed that after the fermentation of PPs by human fecal microbiota, Parabacteroides, Fusicatenibacter, and Parasutterella were significantly enriched. Haloperidol glucuronide and 7-ketodeoxycholic acid generated by these bacteria could be responsible for the increased expression of Alox15 and Pla2g2f and the reduced expression of Cyp1a1 and Hsd17b7 in colon epithelium. The ratio of dihydrotestosterone to estradiol in serum was regulated, and CNP was alleviated. Our results suggested that Parabacteroides, Fusicatenibacter, and Parasutterella could be the essential bacteria in CNP alleviation and their metabolites of PPs 7-ketodeoxycholic acid and haloperidol glucuronide could be the signal molecules of the “gut-prostate axis”.