The amphiphilic cationic polymers that mimic antimicrobial peptides have received increasing attention due to their excellent antibacterial activity. However, the relationship between the structure of cationic polymers and its antibacterial effect remains unclear. In our current work, a series of PEG blocked amphiphilic cationic polymers composed of hydrophobic alkyl-modified and quaternary ammonium salt (QAS) moieties have been prepared. The structure-antibacterial activity relationship of these cationic polymers was investigated against E. coli and S. aureus, including PEGylation, random structure, molecular weights, and the content and lengths of the hydrophobic alkyl side chains. The results indicated that PEGylated random amphiphilic cationic copolymer (mPB(35)/T-57) showed stronger antibacterial activity and better biocompatibility than the random copolymer without PEG (PB33/T-56). Furthermore, mPB(35)/T-57 with appropriate mole fraction of alkyl side chains (f(alkyl) = 0.38), degree of polymerization (DP = 92), and four-carbon hydrophobic alkyl moieties was found to have the optimal structure that revealed the best antibacterial activities against both E. coli (MIC = 8 mu g/mL, selectivity > 250) and S. aureus (MIC = 4 mu g/mL, selectivity > 500). More importantly, mPB(35)/T-57 could effectively eradicate E. coli biofilms by killing the bacteria embedded in the biofilms. Therefore, the structure of mPB(35)/T-57 provided valuable information for improving the antibacterial activity of cationic polymers.