The invention relates to a method used for selectively separating water-soluble nanometer particles. With the adoption of the method, the water-soluble nanometer particles with different dimensions and different sizes can be selectively separated. The method comprises the following specific steps: (a) selecting a surface-active agent: selecting an ionic surface-active agent with opposite charges with the separated nanometer particles as an extracting agent; selecting a surface-active agent containing amine functional groups for electronegative water-soluble nanometer particles; and selecting a surface-active agent containing acids functional groups for electropositive water-soluble nanometer particles; and (b) separating the water-soluble nanometer particles: dispersing the surface-active agents in an oil phase solution and keeping the nanometer particles with large size in water phase by extracting the nanometer particles with small size in the water phase to oil phase by an extracting method so as to realize separation. The separation technology needs no operations of concentration, centrifugation, redispersion, and the like of the conventional separation technology, in addition, the time and the labor are saved, the energy is saved, and the operation is simple in the separation process.