Anxiety-like behavior and social withdrawal induced by obesity and oxidative stress are significant health concerns in contemporary society. Our previously study found that Bacillus amyloliquefaciens SC06 (SC06) decreased the body weight of high-fat diet (HFD)-fed male mice and protected porcine intestinal epithelial cells against oxidative stress. The present study further investigated the effect of SC06 on HFD-induced obesity, anxiety-like behavior and social withdrawal of male mice and explored its mechanism. Results showed that SC06 significantly decreased HFD-induced obesity as evidenced by the decreased body weight, weight of liver and epididymal fat. Meanwhile, SC06 attenuated the anxiety-like behavior of HFD-fed male mice as illustrated by the more exploration time in both the open arms of elevated plus maze and the central area of open field and the reversed their social withdrawal tested in the three-chamber social choice task. SC06 also reduced reactive oxygen species (ROS) concentration and normalized the mitochondrial morphology in the hippocampus. SC06 reduced the systemic inflammation and increased the expression of intestinal tight junctions (ZO-1 and Claudin1). Furthermore, SC06 also altered the microbial diversity and composition, and decreased Firmicutes to Bacteroidetes ratio of HFD-fed male mice. These findings suggest SC06 attenuate HFD-induced anxiety-like behavior and social withdrawal of male mice by attenuating hippocampal oxidation stress, systemic inflammation, dysbiosis and improving intestinal barrier function.