As a natural alternative to antibiotics, probiotics have considerable potential for use in livestock farming. However, the current use of probiotics in livestock poses potential public health risks due to inadequate regulations, including issues such as the inferior quality and dissemination of antibiotic resistance. In this study, 95 non-duplicate commercial probiotic products for livestock were collected from different regions of China. Our findings revealed that the labeling compliance rate for Lactobacillus was the lowest, at just 11%, and approximately 33.3% of the products were contaminated with opportunistic pathogens containing various virulence and antibiotic-resistance genes (ARGs). Isolates of Bacillus and Enterococcus from the products exhibited diverse clonal types and geographical dispersion, whereas certain Enterococcus exhibited close phylogenetic relationships to clones associated with human infectious diseases. Compared with Bacillus and Lactobacillus, Enterococcus exhibited a higher prevalence of ARGs. Specifically, the oxazolidine-resistance gene optrA, which is located on novel transferable plasmids, was found in one isolate of E. faecium. Using chicken models, we observed that the optrA-positive E. faecium disrupts the normal intestinal microbiota in chickens and alters the abundance of intestinal resistome and mobile genetic elements (MGE). Furthermore, metagenomic analysis revealed that the optrA gene can be transferred via transposon IS1216E to commensal intestinal bacteria, including E. cecorum, E. gallinarum, and L. crispatus species. In summary, our study confirms that the probiotic products used in Chinese livestock production present problems such as non-compliance with good manufacturing practice (GMP) production standards and insufficient elucidation of the molecular genetic background of probiotic strains. The widespread use of low-quality Enterococcus strains containing various ARGs as probiotics could disrupt intestinal homeostasis and serve as a reservoir and source of ARGs. We emphasize the importance of carefully evaluating the use of Enterococcus strains as probiotics to avoid potential negative effects on livestock and human health.