It was found that the results of magnetic force microscope (MFM) imaging were different with the probe scanning directions, and the images were often distorted. This paper studied the effect of scanning directions on the MFM imaging, and a method for the distortion compensation was proposed to reduce the errors. In the study, three different scanning directions with the angles of 0°, 45° and 90°, were used to measure the magnetic force distribution of a magnetic sample with a regular structure. The theoretical and experimental results have shown that the scanning direction parallel to the magnetic structure will cause a minimum phase shift difference and lead to a structure distortion. With the proposed compensation method, the distortion structures were corrected and the effect of scanning directions on the MFM imaging was significantly reduced. This work provides a way to obtain the correct images of magnetic structures using an MFM and to improve the imaging quality in a wide range of MFM applications.