This paper proposes a polymer reaction method to introduce a branched structure into cationic polymers' side chains to improve the flocculation performance of the cationic polymer. By using reaction between epoxide compound (EP) and secondary amine in the copolymer (PDD) of methacrylamido propyl trimethyl ammonium chloride (DMC) and diallylamine (DAA), a branched structure was introduced into the side chain of PDD. Three kinds of typical industrial wastewater including sodium humate (NaHA) solution, bentonite suspension, and oilfield produced water (PW) were chosen to be treated by the branched PDD. The pollutants in the three wastewaters had different forms and they were water-soluble organics, solid particles, and liquid droplets, respectively. The effects of flocculant structure and flocculation process on flocculation performance were discussed. The experimental results showed that branched PDD can effectively improve the flocculation performance of PDD. DRE contains an aromatic ring, which may enhance the interaction between PDD-g-DRE and NaHA to promote flocculation. The PDD-g-GTE obtained from the reaction of GTE and PDD contains many hydroxyl groups, which can form hydrogen bonds with the silicon hydroxyl groups on the surface of bentonite to promote flocculation. TDM contains two benzene rings, which made PDD-g-TDM have hydrophobicity. The flocculation can be enhanced because of the hydrophobic interaction between PDD-g-TDM and oil droplets. This work provides a new understanding of the synthesis and performance of branched cationic polymer flocculants.