Antibiotics (AB) are widely abused in medicine and may be a risk factor for mental health. To better understand their effects, we observed mental disorder symptoms in AB-treated mice and patients, and investigated possible mechanisms. Using AB-treated mice, we found obvious anxiety-like behaviors, along with differential gut microbiota (mainly Firmicutes and Bacteroidota), reduced short-chain fatty acids (SCFAs), and disrupted gut-brain lipid metabolism. Acetylcholine decreased in feces, colon wall, serum, and hippocampus of AB-treated mice, and this reduction was significantly correlated with anxiety-like behaviors. Moreover, using AB-treated patients (n = 55), AB-naïve patients (n = 60), and healthy controls (n = 60), we also observed the obvious anxiety symptoms in AB-treated patients, along with differential gut microbiota (mainly Firmicutes), reduced SCFAs, and disrupted lipid metabolism in feces and serum. AB-treated patients showed consistently lower serum and fecal acetylcholine, which was highly correlated with anxiety symptoms. In both AB-treated mice and patients, co-occurrence analysis indicated that the "Bacteroides-acetylcholine" pair may play an important role in AB-induced anxiety. At the species levels, Bacteroides_caecimuris in AB-treated mice and Bacteroides_plebeius in AB-treated patients were both decreased and significantly correlated with acetylcholine. Furthermore, exogenous methacholine (an acetylcholine derivative) intervention effectively alleviated anxiety-like behaviors and suppressed hippocampal microglial activation in AB-treated mice. Together, our findings highlight the harmful effects of aggressive AB treatment on mood and show the potential of acetylcholine or its derivative to reverse this effect.