The invention discloses organic silicon shampoo and a preparation method thereof. The organic silicon shampoo is prepared from a polydimethylsiloxane alcohol emulsion with nano particle size, a composite natural product anti-allergic and itching-relieving extract, sodium methyl cocoyl taurate, cocamidomethyl MEA, glycol distearate, sodium isostearoyl lactylate, stearamide propyl dimethylamine, stearamidopropyl dimethylamine, guar gum hydroxypropyl trimethyl ammonium chloride, cocamidopropyl betaine and other matrix components. The preparation method comprises the following steps: dispersing, mixing and uniformly stirring solid materials, keeping at medium-high temperature for a certain time, cooling, adding low-temperature materials, and uniformly mixing. According to the organic silicon shampoo involved in the technical scheme, the polydimethylsiloxane alcohol nano-emulsion is selected as a main raw material, so that the hydrophilicity of silicone oil is improved, the problem that hydrophobic silicone oil in an existing shampoo product is gathered on scalp is solved, and the beneficial effect of low accumulation of the nano-silicone oil emulsion is achieved.