The invention relates to a preparation method of nanometer in situ composite reaction type organic silicone modified cationic water-based polyurethane and a product thereof. The preparation method comprises the following steps: preparing raw materials of basic monomers, modified monomers and adjuvants; carrying out dewatering pretreatment on mixed polyether glycol; and carrying out pre-polymerization, chain extension, blocking, quaternization and emulsification. So the nanometer in situ composite reaction type organic silicone modified cationic water-based polyurethane is obtained. The method is easy to implement and control, and the nanometer in situ composite reaction type organic silicone modified cationic water-based polyurethane prepared by the method is in a microemulsion state, has a small and uniform emulsion particle size and a good dispersion, and combines merits of organic silicone, polyurethane and inorganic nanometer materials. So the polyurethane prepared in the invention, which can be used to improve the color fastness and pilling resistance of various dyed textiles, allows the textiles to have certain stain resistance, and soft feel of the textiles not to be damaged. Thereby the polyurethane has the advantages of good application performance, wide range of use, safety and environmental protection, and convenient usage.