The invention belongs to the field of benzoxazine resin in polymer synthetic materials and discloses side-chain phthalonitrile modified benzoxazine resin, a preparation method and an application. The resin has a general structural formula shown in a formula I, wherein n is an integer larger than or equal to 1. By means of the characteristic of strong molecular structure design of a benzoxazine monomer, a polymerizable phthalonitrile group is introduced into an aromatic diamine compound through a conventional chemical reaction, then the aromatic diamine compound carrying the phthalonitrile group, paraformaldehyde and bisphenol A have condensation polymerization, and the side-chain phthalonitrile modified benzoxazine resin is prepared. Phthalonitrile which is a polymerizable group is introduced into benzoxazine, so that phthalonitrile can participate in curing, the crosslinking density of polybenzoxazine resin can be further increased, and the thermal stability of polybenzoxazine can be further improved. The preparation method is simple and convenient, a synthesis period is short, the yield is high, and raw materials are easy to obtain.