In this study, six bacterial strains were isolated from the sediment, probiotic fermentation products, and lake sediments, they were identified as Bacillus amyloliquefaciens using genetic evolution analysis, which were named B3, B4, B5, XD3, YF6, and YF8. The comparison of the antibacterial activity, hemolytic activity, and antibiotic sensitivity of six Bacillus amyloliquefaciens strains laid a foundation for the development and application of antimicrobial peptide products. A surface activity assay was used to determine the production of biosurfactants in six Bacillus amyloliquefaciens strains. With Staphylococcus aureus and Escherichia coli as indicator bacteria, their antibacterial activity was determined using the agar diffusion method; the same diffusion method was used to determine the antibiotic susceptibility of Bacillus amyloliquefaciens. The results showed that the six Bacillus amyloliquefaciens strains had obvious biosurface activity, and the bacteria inhibited Staphylococcus aureus and Escherichia coli, from strong to weak: YF8, XD3, B3, B4, YF6, and B5. Strain YF8 had the best broad-spectrum bacteriostatic effect, followed by strain XD3. All Bacillus amyloliquefaciens strains were susceptible to 16 common drugs, except for Bacillus amyloliquefaciens strain YF8, which was intermediate to neomycin. The study shows that Bacillus amyloliquefaciens and secondary metabolites have the ability to produce a variety of active peptides, exert a certain inhibitory effect on common pathogens, and have the potential to develop as animal probiotics.