The removal of single macromolecules impurity is the basis study for the promotion of flocculation technology application in the Chinese herbal medicine solution purification. We applied the flocculation process to remove gelatinized starch in solution. Three types of cationic polyacrylamide (CPAM) with different charge density were used for flocculation of gelatinized starch solution. The flocculation performance was evaluated in terms of the amylose removal ratio (AMRR), the amylopectin removal ratio (APRR), total starch removal ratio (TSRR) and supernatant turbidity (ST). The flocs were characterized by sedimentation performance, Fourier transform infrared (FTIR), scanning electron microscope (SEM) and X-ray photoelectric spectroscopy (XPS) method. The experimental results show that the flocculant CN15 has the best performance for gelatinized starch flocculation among three flocculants. According to the characterization analysis, the flocs exhibited an obvious network structure, and it is concluded that hydrogen bonding between N-H in CPAM and C-O in the starch and bridging flocculation played the essential roles in flocculation of the gelatinized starch.