The invention belongs to the field of high polymer material research, and provides an organic silicon modified thermoplastic polyurethane elastomer (TPU) in order to overcome the defects of poor temperature resistance and hydrophobic property of the existing TPU. The elastomer consists of the following components in parts by weight: 20-60 parts of macromolecular dihydric alcohol, 2-10 parts of terminal hydroxyalkyl end-blocked polydimethylsiloxane, 10-20 parts of diisocyanate, 2-8 parts of a micromolecular chain extender, 0.1-0.5 part of a catalyst, 0.1-0.5 part of an antioxidant and 0.1-0.5 part of an ultraviolet light absorber. Due to the unique chemical structure and composition, organic silicon has a series of excellent properties, such as high temperature and low temperature resistance and hydrophobic property, which just can make up the defects of the TPU. The invention also provides a preparation method of the elastomer, the preparation method adopts a prepolymer two-step process and is less in side reaction, and the prepared TPU is good in structural regularity.