The invention provides a composite antibacterial agent and a preparation method thereof. The antibacterial agent is prepared by the following steps of: (1) mixing water-soluble polyguanidine inorganic acid salt or aqueous solution of organic acid salt and aqueous solution of water-soluble silicate, and uniformly stirring to obtain a mixture; (2) adding aqueous solution of water-soluble metal saltinto the mixture obtained in the step (1), and stirring to obtain a sediment; and (3) drying and crushing the sediment obtained in the step (2). The composite antibacterial agent has the advantages of water insolubility, high sterilization efficiency, no influence on product color and the like, and can be applied to antibacterial plastic, an antibacterial coating, an antibacterial fiber or antibacterial rubber which has high requirement on water resistance; and the preparation method is simple and contributes to industrialization.