This paper presents a detailed analysis on the influence of misalignment errors of optical components in an orthogonal two-axis Lloyd's mirror interferometer, which can fabricate two-dimensional grating structures in a single exposure. In an ideal condition, defect-free two-dimensional grating structures can be fabricated by the interferometer. However, in a real case, visible stripes caused by misalignment errors of the optical components in the interferometer always appear on the fabricated grating structures. In this paper, theoretical analysis and experiments are carried out to analyze the influences of the misalignment errors of the optical components in the orthogonal two-axis Lloyd's mirror interferometer.