The invention provides a preparation method of an interpenetrating-network-structure water-based polyurethane nano composite material. The preparation method comprises the following steps: 1) carrying out vacuum dehydration treatment on polymer polylol and hydrophilic functional monomer; 2) adding a catalyst and diisocyanate, reacting at room temperature for 0.5-2 hours, heating to 60-80 DEG C, and carrying out the reaction for 1-5 hours while keeping the temperature; 3) cooling to 40-50 DEG C, adding a chain extender, and carrying out the reaction for 2-4 hours while keeping the temperature; 4) heating to 60-70 DEG C, and adding a reactive monomer for termination; 5) cooling to 30-50 DEG C, and adding a neutralizer to regulate the pH value; 6) heating to 60 DEG C, dropwise adding deionized water, and dispersing by stirring; and 7) heating to 60-65 DEG C, dropwise adding an initiator water solution and a nucleation monomer, carrying out programmed heating, and carrying out the reaction while keeping the temperature, thereby obtaining the interpenetrating-network-structure water-based polyurethane nano composite material. The method effectively solves the problem of VOC (volatile organic compound) discharge. The nano composite material has the characteristics in both the core-shell structure and the interpenetrating network structure, and thus, has favorable mechanical properties. The adopted continuous-process synthesis technique is beneficial to enhancing the production efficiency.