The invention relates to a preparation method of a 3, 3-difluoro-4-aminopiperidine compound shown as a formula (I) and a derivative thereof, and the compound has the following structure: wherein R ishydrogen, C1-C9 alkyl, aryl, benzyl, CF3CO, R2CO or R3OCO; wherein R1 is C1-C9 alkyl, aryl or benzyl, R2 is C1-C9 alkyl, aryl or benzyl, and R3 is C1-C9 alkyl, aryl or benzyl; the preparation method of the compound and the derivative thereof comprises the following steps: starting from a 3, 3-difluoro-4-hydroxypiperidine structure, introducing a sulfonyloxy leaving group, and carrying out azido (N3) group substitution and azido reduction. According to the preparation method, optically pure 3, 3-difluoro-4-hydroxypiperidine and derivatives thereof are used as starting materials, and the optically pure 3, 3-difluoro-4-aminopiperidine and derivatives thereof with reversed configurations are finally obtained through the conversion.