The invention discloses a preparation method of an organic silicon modified collagen membrane. The method comprises the steps: firstly, completely dissolving animal collagen by using an acetic acid solutionto be prepared into a collagen solution; after removing bubbles, carrying out flow casting to form a membrane, and drying the membrane to obtain a white transparent collagen membrane; and then, placing the prepared collagen membrane into an inorganic alkaline solution, adding organic silicon, and carrying out a reaction at normal temperature, and after ending the reaction, washing the surface, and drying the collagen membrane to obtain a modified collagen membrane. The method is simple, convenient, very short in time consumption, low in equipment requirement and capable of shortening the preparation period and reducing the production cost; in addition, the hydrophobicity of the collagen membrane is greatly improved, an obstacle that the collagen membrane is applied to the commerce is basically eliminated, and the phenomenon that an exogenous toxic chemical substance enters the collagen membrane to affect the edibility of the collagen membrane is avoided.