STEM nano-moire can achieve high-precision deformation measurement in a large field of view. In scanning moire fringe technology, the scanning line and magnification of the existing transmission electron microscope (TEM) cannot be changed continuously. The frequency of the crystal lattice is often difficult to match with the fixed frequency of the scanning line, resulting in mostly too dense fringes that cannot be directly observed; thus, the calculation error is relatively large. This problem exists in both the STEM moire method and the multiplication moire method. Herein, we propose the STEM secondary nano-moire method, i.e., a digital grating of similar frequency is superimposed on or sampling the primary moire fringe or multiplication moire to form the secondary moire. The formation principle of the secondary moire is analyzed in detail, with deduced theoretical relations for measuring the strain of STEM secondary nano-moire fringe. The advantages of sampling secondary moire and digital secondary moire are compared. The optimal sampling interpolation function is obtained through error analysis. This method expands the application range of the STEM moire method and has better practicability. Finally, the STEM secondary nano-moire is used to accurately measure the strain field at the Si/Ge heterostructure interface, and the theoretical strain field calculated by the dislocation model is analyzed and compared. The obtained results are more compatible with the P-N dislocation model. Our work provides a practical method for the accurate evaluation of the interface characteristics of heterostructures, which is an important basis for judging the photoelectric performance of the entire device and the optimal design of the heterostructures.