Fourier ptychographic microscopy (FPM) is a newly developed computational imaging technique that can provide gigapixel images with both high resolution (HR) and wide field of view (FOV). However, there are two possible reasons for position misalignment, which induce a degradation of the reconstructed image. The first one is the position misalignment of the LED array, which can largely be eliminated during the experimental system building process. The more important one is the segment-dependent position misalignment. Note that, this segment-dependent positional misalignment still exists, even after we correct the central coordinates of every small segment. In this paper, we carefully analyze this segment-dependent misalignment and find that this global shift matters more, compared with the rotational misalignments. According to this fact, we propose a robust and fast method to correct the two factors of position misalignment of the FPM, termed as misalignment correction for the FPM misalignment correction (mcFPM). Although different regions in the FOV have different sensitivities to the position misalignment, the experimental results show that the mcFPM is robust with respect to the elimination of each region. Compared with the state-of-the-art methods, the mcFPM is much faster.