Sub-micron sized phenolic epoxy resin waterborne particles were prepared by phase inversion emulsification.Micro-phase separation occurred during the curing process at high temperature. The as-prepared samples possessed one glass transition temperature (Tg) and two exothermal processes during DSC heating scannings. After being thermally treated above the exothermal peak temperature, they possessed two glass transition temperatures with the disappearance of exothermal peaks, whilst a core/shell structure was formed. This was likely related with the outward diffusion of reactive oligomers to the outer layer of particles.