The invention provides an epoxy modified polyphenylene ether resin, the epoxy modified polyphenylene ether resin possesses a structural unit shown in a formula (I), and a preparation method comprises the following steps 100 parts of solid polyphenylene ether resin adds a polymerization reaction solvent for dissolving into a liquid polyphenylene ether resin solution, and then 5-60 parts of epoxy resin and 0.001-5 parts of a catalyst are added in the solution, stirred and mixed at the temperature of 80-140 DEG C for 1- 3 hours to obtain a pre-polymerization solution. The invention also discloses a resin composition containing the epoxy modified polyphenylene ethesr resin, and an application in preparation of printed circuit board. The epoxy modified polyphenylene ether resin composition has the advantages of excellent glass fiber cloth impregnation, simple preparation process, high efficiency, environmental protection and high product purity controllability; can be used for making a laminated material and a copper clad pressure plate, possess excellent heat resistance and dielectric properties, and is in favor of signal transmission of high frequency circuit board.