In this paper, a new nano-moiré method using scanning tunneling microscope (STM) is proposed. This method is capable of measuring nanoscopic deformation of matter. The formation mechanism of the STM moiré fringe and the phase shifting technique used in STM moiré fringes are explained in details. Typical experiments are conducted with the crystal lattices of freshly cleaved highly oriented pyrolytic graphite, are used as specimen grating, to generate STM moiré fringe patterns. Phase shifting is realized in four steps from 0 to 2 π by controlling the PZT in the STM system to shift the specimen in the vertical direction. This method provides a new way for disposal of moiré fringes pattern in the nano-moiré measurement.