Escherichia coli O157:H7 is a pathogen that commonly causes foodborne illness and represents a health hazard to consumers. The combined use of synergistic antimicrobial peptides (AMPs) is a promising way to improve the microbiological safety of foods. In this study, we detected the synergistic interactions between thanatin and BF-15a3 to reduce their usage and obtain more efficient antibacterial activity. The minimal inhibitory concentrations (MICs) of thanatin and BF-15a3 against 49 E. coli O157:H7 strains were ranged from 2 to 8 μg/mL and 4-32 μg/mL, showed a general inhibitory effect on E. coli O157:H7 strains, respectively, even multidrug-resistant strains. Their fractional inhibitory concentration index (FICI) was 0.375, which suggested that their combination presented synergistic antibacterial effect against E. coli O157:H7. The killing kinetic curves indicated that the 0.25 × MIC combination had equivalent bactericidal effects to 1 × MIC thanatin or BF-15a3. When AMP combinations were used to treat eukaryotic cells to evaluate the hemolytic characteristics against rabbit erythrocytes and cytotoxicity against human embryonic kidney 293T (HEK-293T) cells and intestinal porcine enterocyte J2 (IPEC-J2) cells, no magnified adverse effects were observed, exhibiting higher specificity to bacteria and lower toxicity to eukaryotic cells. Compared with bacteriostasis of thanatin or BF-15a3 alone, the proportion of membrane-damaged bacteria treated with the synergetic combination did not appear a significant rise, interestingly the Zeta potential of them greatly decreased and their cell membrane permeability significantly increased. Besides, more release of ions and cytoplasm were detected, confirming a more severe loss of membrane integrity. These results suggested that the synergistic action mode of thanatin and BF-15a3 is likely attributed to damage aggravation to E. coli membrane. When applying in fresh-cut lettuce and cucumber, their combination allowed for 2.5 log CFU/piece reductions of E. coli O157:H7 in 24 h. In conclusion, the combination of thanatin and BF-15a3 showed excellent synthetic efficacy to kill E. coli O157:H7 in vitro under lower MICs than single use of them.