To address the complexity and limitations of existing calibration methods for Scanning Probe Microscope (SPM), this article proposed a novel SPM calibration method by using a 2D micro?scale orthogonal lattice standard and peak detection (PD) method of the pitch center coordinates based on cross?correlation / convolution (CC) filtering of raster?scanned images. The geometric errors of motion include positional deviations Δx and Δy, straightness deviations δy and δx along x?axis and y?axis respectively, and the orthogonality deviation γ_xy between the two axes. The calibration factors C_x and C_y were calculated based on the number of pixels scanned on the x?axis and y?axis, scanning range, average pitch of standard grid metrology verification, and average grid spacing. Through case study, an AFM was calibrated using an orthogonal lattice standard with a nominal pitch of 10 μm, resulting in C_x and C_y values of 0.925 and 1.050, respectively, and an orthogonal deviation γ_xy of 0.015°. The expanded uncertainty of calibration for this AFM was 0.33 μm(k = 2.56). This SPM calibration method will promote the implementation and execution of SPM calibration standard documents, and has technical reference value for the development and performance evaluation of SPM instruments.