Cationic conjugated polymers (CCPs) have attracted more and more attention in antibacteria and tumor treatment based on photodynamic therapy (PDT). However, the main chain structure-antibacterial activities relationship has been rarely reported. Herein, we designed and synthesized four cationic conjugated polymers: one poly(fluorine phenylene) derivative (PFP) and three poly(fluorene-co-phenylene ethynylene) derivatives (PFE-1, PFE-CN-2, and PFE-NP-3). PFP and PFE-1 have the same side chains but bear different conjugated backbones. PFE-CN-2 (pi-A) and PFE-NP-3 (A-pi-A) are modified with electron-donating and/or electron-withdrawing groups. Three PFEs can produce reactive oxygen species (ROS) faster than PFP. The order of antibacterial activities of the four CCPs is as follows: PFE-CN-2 > PFE-1 >> PFE-NP-3 approximate to PFP, which is coincident with the generation rate of ROS. In addition, CCPs with D-pi-A structure is more advantageous than A-pi-A in ROS production and in antibacterial performance. These results provide an important base for designing more efficient PDT agents for antibacteria and antitumor.