In the present study, the synergetic effect and mechanism of ultrasound (US) and slightly acidic electrolyzed water (SAEW) on the inactivation of Escherichia coli (E. coli) were evaluated. The results showed that US combined with SAEW treatment showed higher sanitizing efficacy for reducing E. coli than US and SAEW alone treatment. US and US combined with SAEW treatments resulted in smaller particle size of E. coli compared to the control and SAEW treatment. In addition, US combined with SAEW treatment induced the highest potassium leakage. However, the highest protein leakage was recorded in US treatment. Moreover, scanning and transmission electron microscopy analysis revealed that the greatest damage of the appearance and ultrastructure of E. coli was achieved after US combined with SAEW treatment. The synergetic effect was also confirmed by CLSM analysis. Fluorescence spectroscopy suggested that treatments of US, SAEW, and US combined with SAEW changed protein conformation of E. coli. Overall, the present study demonstrated that the sterilization mechanism of US combined with SAEW treatment was decreasing the particle size and disrupting the permeability of cell membrane and the cytoplasmic ultrastructure as well as changing protein conformation of E. coli.