In this study we investigate the synergistic effect of low frequency ultrasonication (14, 22, and 47 kHz) on antimicrobial activity of Cecropin P1 against Escherichia coli. The hypothesis was tested by comparing three different treatments (1) ultrasonication only (2) Cecropin P1 only (3) combination of both. The results showed that the combined treatment deactivate E. coli more efficiently by six order of magnitude. The mechanism of membrane permeabilization due to Cecropin P1 is also investigated using dye leakage experiment. The result indicated pore formation and carpet mechanism. Finally, a mathematical modeling is proposed to explain the synergistic effect, allowing us to make better prediction for cell deactivation.