The invention discloses 5'-amino-2',5'-dideoxynucleotide phospholipid molecules, and a preparation method and an application thereof. The 5'-amino-2',5'-dideoxynucleotide phospholipid molecules provided by the invention have an amphiphilic structure represented by the formula (I). 5'-amino-2',5'-dideoxynucleoside is adopted as a hydrophilic head, and glycerol fatty ether connected by using a phosphate bond is adopted as a hydrophobic tail, such that an amphiphilic molecule is formed. The Base group is common purine and pyrimidine bases, and R group is saturated or unsaturated aliphatic carbon chain. In a water-phase solvent, the dideoxynucleotide phospholipid molecule can form a plurality of supramolecular structures including multi-layer film structure, lipid structure, fibrous structure, and hydrogel. Therefore, 5'-amino-2',5'-dideoxynucleotide phospholipid molecules have certain potential to be used as aggregation, trapping, loading, or carrying type nucleic acid medicines, and can be used as a high-efficiency biological material for mediating transmembrane of nucleic acid medicines.