Provided is a method for preparing a polymer nano-composite, more particularly, an economical method for preparing a polymer nano-composite with improved properties via a single process of organic treatment of a layered clay mineral and dispersion in a rubber latex material at a pH where both the rubber latex material and the layered clay mineral are stabilized. The provided method for preparing a polymer nano-composite allows effective dispersion without using an organic modification process for improving dispersibility of the layered clay mineral in resin. Thus prepared polymer nano-composite exhibits superior mechanical property and may be usefully applied for automobile interior and exterior materials.