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.