The present invention relates to a multilayer polymer latex comprising a seed, a rubbery core surrounding the seed, and a shell surrounding the rubbery core, in which the seed comprises a vinyl unit, a hydrophilic unit and a crosslinker unit, as well as a preparation method thereof. The present invention can provide an acrylic polymer latex and a diene polymer latex, depending on materials constituting the core and the shell. In the present invention, the seed containing a vinyl unit, a hydrophilic unit and a crosslinker unit, and the rubbery core, are used for the preparation of the polymer latex. This can increase the rubber content of the polymer latex, thus improving the impact resistance of the polymer latex, and at the same time, reduce the viscosity of the polymer latex so as to improve the long-term workability of the polymer latex upon spray drying. Thus, polymer powder prepared from the polymer latex is excellent in not only impact resistance but also flow properties.