The invention discloses an operation method of a three-dimensional flash memory array unit with variable programming stages. The operation method comprises the following steps: S1, receiving an erasing operation instruction and address information; S2, erasing the selected block structure; S3, receiving a multi-level programming instruction and address information; S4, judging whether the addressoverflows or not, if yes, entering S5, otherwise, receiving programming level information of the target unit, and entering S6; S5, completing the programming operation of the selected block structure,and ending; S6, performing multi-level programming operation on the current flash memory unit according to the multi-level programming instruction, the address information and the programming level information of the target unit; S7, judging whether the difference of the threshold voltages is not smaller than the preset minimum interval voltage or not, if yes, changing the address information, entering S3, and performing the programming operation of the next flash memory unit; And otherwise, carrying out multi-level programming operation on the current flash memory unit for no more than the preset number of times again. The flash memory unit is subjected to target stage number programming, the threshold voltage of the flash memory unit is accurate to the preset value, and therefore the data state of the flash memory unit is accurately controlled.