The objective of this study was to investigate the effect of different counterions on the flocculation of cationic polymer flocculants and to obtain new high efficient flocculants by modifying polydiallyldimethylammonium chloride (PDADMAC) with different counterions. The effect of nitrate or sulfate as counterions on flocculation properties of polydiallyidimethylammonium salts (PDADMAX) was investigated in the conventional jar test procedure by using optical monitoring technique and zeta potential measurement. Moreover, in order to indicate the flocculation mechanism of PDADMAX having different counterions, the effect of counterions on the solution property and adsorption conformation of PDADMAX was studied by reduced viscosity and atomic force microscopy (AFM). The experiment results show that counterions have a significantly different effect on PDADMAX flocculation where "adsorption charge neutralization action" and "adsorption bridging action" play different parts. PDADMAX having NO3-has stronger "adsorption charge neutralization action" and its turbidity removal is 98%, whereas PDADMAX having SO42- has stronger "adsorption bridging action", as well as the wider optimum dosage and larger floc size. In particular, the flocculation efficiency of PDADMAX having different contents of SO42- or NO3- different. The optimum content of SO42- or NO3- is 20%.