To inactivate both standard strains as well as antibiotic-resistant strains with minimum damage to host cells, three new pyridyl cationic-modified benzylidene cyclopentanone photosensitizers (PSs), P1 (with one cationic group), P2 (with two cationic groups bilaterally), and P3 (with two cationic groups unilaterally) were synthesized and characterized. Their selective uptakes by bacteria over HepG2 cells and their photodynamic inactivation efficiencies against Staphylococcus aureus (ATCC 6538), Escherichia coli (ATCC 25922), and the drug-resistant Escherichia coli (CA-31) were studied using methylene blue (MB) and hematoporphyrin monomethyl ether (HMME) as references. The results showed that the uptake amounts of P1, P2, and P3 by all strains were at least 2, 20, and 18 times more than those by HepG2 cells, respectively. All PSs exhibited good antimicrobial photodynamic therapy (aPDT) effects towards three strains with low concentrations of ≤ 8.0 μM, while MB was invalid towards three strains and HMME was invalid toward Escherichia coli (CA-31) with the concentration up to 32.0 μM. Especially, the minimum inhibitory concentrations (MICs) of P3 against these strains were all ≤ 2.0 μM, under which about 94% HepG2 cells were still alive, indicating P3 had high aPDT selectivity for bacterial cells over mammalian cells. The relationships between structure and antimicrobial properties of these cationic PSs were discussed to reveal their high photodynamic inactivation selectivity of bacterial cells.