Abstract This paper presented a novel scanning probe microscope (SPM) error measurement 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 images raster-scanned by SPMs. The geometric errors of motion and drifting rate in x-y plane are measured. Geometric errors include positional deviations E x x and E y y , straightness deviations E x y and E y x along x- and y-axis respectively, and the orthogonality deviation E o x y 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 lattice from metrological verification certification, and average lattice pitch calculated by using PD method. Through case study, the errors of an AFM was measured 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, an orthogonal deviation E o x y of 0.015°, and the maximum drift rate of the x-axis and y-axis is −366.21 nm min−1 and −317.38 nm min−1, respectively. The new error measurement method of SPMs provides technical reference for the development and performance improvement of SPM instruments.