Vacuum cooling often results in the penetration of pathogenic bacteria into vegetable stomata, making conventional washing methods ineffective. To remove Escherichia coli that penetrates the stomata of lettuce, a vacuum-ultrasonic (VC-US) composite cleaning method was used at three evacuation rates: α1 (0.467 3/min), α2 (0.323 5/min), and α3 (0.161 7/min). The effectiveness of VC-US and its impact on lettuce quality were evaluated by measuring the colony counts and relevant physicochemical properties before and after cleaning as well as the changes in these indicators during storage. The results showed that the α3 group reduced E. coli counts inside lettuce from 4.33 to 1.47 log10 CFU/cm2, which was significantly more effective than the α1 and α2 groups, whose E. coli counts were reduced to 2.03 and 1.92 log10 CFU/cm2, respectively (P<0.05). After two days of storage, L* and b* values of the α3 group were significantly lower than those of the α1 group (P<0.05), whereas the a* value was slightly higher; however, no significant difference was detected when compared with the α2 group (P>0.05). Chlorophyll and vitamin C contents showed no significant differences among the three treatment groups (P>0.05). Additionally, the weight loss rate was significantly lower in the α3 group (-19.89%) than in the α1 (-0.18%) and α2 (-19.03%) groups (P<0.05). Collectively, these findings indicate that VC-US cleaning with a lower evacuation rate is more effective in removing E. coli inside lettuce without significantly affecting its quality, thus providing theoretical support and practical value for the application of VC-US technology in removing internal pathogens from vegetables.