In this investigation, we propose a flexible structured illumination microscope (FSIM) to eliminate mechanical moving parts for the phase shifts in the spatial pattern and longitudinal scanning of the specimen. In order to prevent these mechanical motions, we adopt a focus-tunable lens and digital micromirror device (DMD) to replace the lateral motion of the pattern and the scanning of the specimen, respectively, which leads to the enhancement of rapid and precise measurement results for measuring the 3D surface profile of specimens. To realize the proposed system, two types of flexible structured illumination microscopes, Macro and micro types, were constructed and their performances were verified with a plane mirror and step height specimens.