A method for manufacturing logic device isolation in an embedded storage process, removing the pad silicon nitride and floating gate polysilicon layer in a shallow trench isolation area and retaining the floating gate oxide layer; depositing acid etching silicon nitride; removing the acid etching silicon nitride at the bottom of the shallow trench isolation and a portion of the silicon substrate adjacent to and under the shallow trench isolation, to form a trench and retain the acid etching silicon nitride on a side of the floating gate polysilicon layer close to the shallow trench isolation; remove the acid etching silicon nitride on the side of the floating gate polysilicon layer close to the shallow trench isolation.