The invention discloses a method for producing cordycepin with self-assembly silicon plastid electrostatic spinning fibrous membrane immobilized cells. The method comprises the following steps that Chinese caterpillar fungus protoplasts are wrapped into a stable silicon plastid formed by organic-inorganic hybrid lipids by utilizing a electrostatic self-assembly method; chitosan, polyvinyl alcoholand polyethylene oxide are completely dissolved into an acetic acid solution, glycerol is added, then silicon plastid is added, a nanometer fibrous membrane is prepared with electrostatic spinning, the nanometer fibrous membrane is rolled, and the rolled nanometer fibrous membrane is charged in a chromatography column; a mixed solution of glucose, ribose, potassium dihydrogen phosphate, magnesiumsulfate, yeast powder and adenine is prepared, filtering and bacteria removal are carried out on the mixed solution, the mixed solution flows through the chromatography column at a certain flow rate,gas is introduced at the lower part of the chromatography column at the same time, and through detection, an effluent contains the cordycepin. The method with the immobilized cells has the characteristics of high efficiency, bacterium contamination resistance, high yield and high concentration of a product and is beneficial to separation and purification of a subsequent product.