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A development of coagulation-flocculation is to improve flocculation performance of organic polymer flocculants. It is hopefully achieved via optimizing molecular structure of flocculants. Herein, molecular structure of cationic organic polymer flocculants, P(AM-DAC), was regulated through adjusting the length of cationic block on the molecular chain of P(AM-DAC). The effect of block length of P(AM-DAC) on its characteristics, flocculation performances and flocculation mechanisms in water treatment was rarely considered. The moderate template contributed to P(AM-DAC) (10_4:1) possessing the longest cationic block structure, largest molecular weight and best thermal stability compared with other P(AM-DAC). Molecular dynamics (MD) simulation and the flocculation experiments predicted and confirmed that P(AM-DAC) (10_4:1) performed the best in the treatment of colloidal particles and dyes in terms of removal efficiencies and floc characteristics since the centralized cationic block structure enhanced the interaction among P(AM-DAC) (10_4:1) and pollutants and further improved charge neutralization and bridging of P(AM-DAC) (10_4:1). [Display omitted] • P(AM-DAC) with different block lengths were adjusted via various template sizes. • P(AM-DAC) (10_4:1) owned the longest block length as moderate molecular weight of template. • The strong interaction between P(AM-DAC) (10_4:1) and pollutants was confirmed by MD. • P(AM-DAC) (10_4:1) with concentrated cationic blocks had the best flocculation performance. [ABSTRACT FROM AUTHOR]