Weaning transition in porcine industry is marked by nutritional, microbial, and psychological stresses that can impair growth and development. Accumulating evidence indicates that weaning-related stress not only disrupts gut microbial homeostasis but impairs gut-brain axis signaling through activation of stress-related neuroendocrine pathways. However, current interventions have largely focused on improving growth performance or enteric symptoms, while integrated strategies targeting the gut-brain-microbiome axis remain limited. Next-generation probiotics (NGPs) such as Bacteroides fragilis have been reported to exert beneficial effects on both intestinal health and brain function, positioning them as promising candidates for alleviating weaning stress. However, their practical application remains challenging due to the strict anaerobic nature. In this study, we investigated that a porcine-derived heat-killed B. fragilis SLAM_BAF01 exerts beneficial effects under weaning stress through gut-brain-microbiome modulation, thereby enabling a more stable and scalable application. First, to investigate the relationship within the gut-brain-microbiome axis under weaning stress conditions, we employed a fecal microbiota transplantation (FMT)-based mouse model and a physiologically relevant weaning pig model. Multi-omics analyses were conducted to characterize microbial and host responses. B. fragilis SLAM_BAF01 exhibited acid and bile tolerance, preserved structural integrity, and lacked enterotoxicity. In the mouse FMT model, heat-killed SLAM_BAF01 positively modulated gut microbial composition, reinforced intestinal barrier function, and attenuated stress-related responses. Especially, brain γ-aminobutyric acid (GABA) levels increased by 150 %, while serum corticosterone levels were reduced by 17 % compared with the control. In the weaning pig model, heat-killed SLAM_BAF01 improved growth performance by 7 % and significantly reduced inflammation and stress markers. These findings demonstrate that heat-killed postbiotic B. fragilis SLAM_BAF01 as a promising candidate capable of mitigating weaning-associated stress through enhancing gut-brain-microbiome axis function in porcine industry.