The pitch and orthogonality of two-dimensional (2-D) gratings were measured using a metrological atomic force microscope (MAFM), and the measurement uncertainty was analyzed. Gratings are typical standard devices for the calibration of precision microscopes, Since the magnification and orthogonality in two perpendicular axes of microscopes can be calibrated simultaneously using 2-D gratings, it is important to certify the pitch and orthogonality of such gratings accurately for nanometrology. In the measurement of 2-D gratings, the MAFM can be used effectively for its nanometric resolution and uncertainty, but a new measurement scheme is required to overcome limitations such as thermal drift and slow scan speed. Two types of 2-D gratings with nominal pitches of 300 and 1000 nm were measured using line scans to determine the pitch measurement in each direction. The expanded uncertainties (k = 2) of the measured pitch values were less than 0.2 and 0.4 nm for each specimen, and the measured orthogonality values were less than $0.09^{circ}$ and $0.05^{circ}$, respectively. The experimental results measured using the MAFM and optical diffractometer agreed closely within the expanded uncertainty of the MAFM. We also propose an additional scheme for measuring 2-D gratings to increase the accuracy of calculated peak positions, which will be the subject of future study.