In this study, the temporal evolution and electrical characteristics of atmospheric pressure cold plasma jet (APPJ) structures with different quartz tube wall thicknesses that used AC power were investigated via experimentation and simulation. The percentage increase of electron density based on the wall thickness was investigated. Based on the optimal electric field intensity distribution and flow field distribution, the quartz tube with the optimal wall thickness improved the electron density. We applied the optimized APPJ structures to inactivate E. coli. We demonstrated that the APPJ structures with thin-walled quartz tubes had better inactivation characteristics than those with thick-walled structures regardless of the duration of treatment. The electron density properties of APPJ structures with different quartz tube wall thicknesses have a prominent impact on the improvement in the killing rate in the sterilization processes.