The invention discloses a high molecular weight guanidine salt and polybasic amine antibiosis type polymer and a preparation method and the application thereof. The polymer comprises a repeated unit structure as right, wherein, X1 and X2 are the same or different polybasic amines; Y is Cl<->, NO3<->, HCO3<-> or H2PO4<->; Z is polyprotic acid, polyprotic acid anhydride or multielement ester. When in preparation, the mixture of polynary amine and guanidine salt is heated for reaction, and then polyprotic acid, polyprotic acid anhydride or multielement ester is added, and the temperature is continuously raised for reaction. The invention solves the problem that the polybasic amine and the guanidine salt react through a main body, thereby being difficulty to obtain a higher molecular weight polymer. In lower reaction temperature and shorter reaction time, by the chain expanding reaction to a polynary amine and guanidine salt prepolymer by the polyfunctionality substance, the high molecular weight guanidine salt and polybasic amine antibiosis polymer is formed. The polymer can be used as the anti fungus agent of the fiber product, the paper product, the non-weaving product and the tissue, etc.