The invention discloses a polyquaternium polymer emulsion antibacterial agent, a preparation method thereof and an application thereof. The polyquaternium polymer emulsion antibacterial agent comprises the following raw material components in parts by weight: 0.3-3 parts of cationic antibacterial monomer, 0.3-0.7 part of initiator, 60-80 parts of water, 1-14 parts of hard monomer, 1-17 parts of soft monomer, 0.1-1 part of waterproof functional monomer, 0.1-0.3 part of crosslinking functional monomer and 0.1-0.7 part of adhesion functional monomer. According to the technical scheme of the invention, the soap-free emulsion synthesis technique is adopted, so that no emulsifier is adopted. The water oxygen-rich pollution can be reduced. The obtained polyquaternium polymer emulsion antibacterial agent is strong in antibacterial performance, free of dissolution, and good in durability. The polyquaternium polymer emulsion antibacterial agent can make up the blank in the market and can be widely applied to the antibacterial treatment of fabric antibacterial finishing, automotive metal and plastic decorative materials, floors, ceramic products and home appliances. Meanwhile, the polyquaternium polymer emulsion antibacterial agent can be applied to the antibacterial and preservative treatment of aqueous coatings, inks, adhesives and the like.