The invention discloses a cationic functional vinyl chloride polymer and a preparation method thereof. The functional vinyl chloride polymer is a cationic functional vinyl chloride polymer prepared by the steps of: taking a chlorine-containing monomer, a graftable active monomer and a hydrophilic functional monomer as copolymerization monomers, firstly polymerizing, in a water phase dispersion system, the copolymerization monomers into an active precursor polymer of which the main chain contains an atom transfer free radical polymerization active side group, then initiating a cationic functional monomer by using the active side group on a solid liquid interface to perform interface atom transfer free radical polymerization, and performing polymerization to form the cationic functional vinyl chloride polymer containing a cationic type side chain. The cationic type side chain contains quaternary ammonium salt type and quaternary phosphonium salt type groups, has a very strong charge positive electrical property, and enables the polymer to have very strong antibacterial performance, hydrophilic performance and anion exchange absorbing performance, and the polymer can be applied separately to preparation or together with other resin to blending preparation of a high-hydrophilicity antibacterial separation membrane product, a battery diaphragm, an anion exchange adsorbing material and an antibacterial coating, so that the application range of vinyl chloride type polymers is greatly broadened; and in comparison with an existing material, the polymer is good in hydrophilicity, is antibacterial, and is good in application prospect.