To address the complexity and limitations of existing calibration methods for Scanning Probe Microscope (SPM), this paper 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 and , straightness deviations and along x- and y-axis respectively, and the orthogonality deviation between the two axes. The calibration factors and were calculated based on the number of pixels scanned on the x-axis and y-axis, scanning range, average pitch of standard lattice from metrological verification certification, and average lattice pitch calculated by using PD method. Through case study, an AFM was calibrated using an orthogonal lattice standard with a nominal pitch of 10 μm, resulting in and values of 0.925 and 1.050, respectively, and an orthogonal deviation of 0.015. The new SPM calibration method may improve or fill-in the recommended but not yet completely implemented methods in the international standard document.