A method for measuring distorted illumination patterns and correcting image artifacts in structured illumination microscopy. The method includes the steps of generating an illumination pattern by interfering multiple beams, modulating a scanning speed or an intensity of a scanning laser, or projecting a mask onto an object; taking multiple exposures of the object with the illumination pattern shifting in phase; and applying Fourier transform to the multiple exposures to produce multiple raw images. Thereafter, the multiple raw images are used to form and then solve a linear equation set to obtain multiple portions of a Fourier space image of the object. A circular 2-D low pass filter and a Fourier Transform are then applied to the portions. A pattern distortion phase map is calculated and then corrected by making a coefficient matrix of the linear equation set varying in phase, which is solved in the spatial domain.