The invention discloses an organic silicon modified waterborne polyurethane leather coating agent which comprises the following raw materials in parts by weight: 30-50 parts of polyether polyol, 10-30 parts of isocyanate, 1-8 parts of castor oil, 0.1-11 parts of end hydroxyalkyl polydimethylsiloxane, 0.01-1 part of a catalyst, 1-10 parts of a hydrophilic chain extender, 5-25 parts of an organic solvent, 1-5 parts of a salt-forming agent, 1-3 parts of a small-molecule chain extender and 120-250 parts of deionized water. Correspondingly, the invention further provides a method for preparing the organic silicon modified waterborne polyurethane leather coating agent. By adopting the organic silicon modified waterborne polyurethane leather coating agent, properties such as the water resistance, the cold resistance, the solvent resistance and the surface property of synthesized waterborne polyurethane are all remarkably improved, the process is simple, the operation is convenient, the prepared emulsion is uniform and stable, no sediment is generated in the water dispersion and storage process, a coating film is transparent and bright, and the application prospect in leather coating is wide.