An illumination system for a metrology apparatus that can achieve illumination spatial profile flexibility, high polarization extinction ratio, and high contrast. The illumination system includes a polarizing beam splitter (PBS), an illumination mode selector (IMS), and a reflective spatial light modulator (SLM). The PBS divides an illumination beam into sub-beams. The IMS has a plurality of apertures that transmits at least one sub-beam and may be arranged in multiple illumination positions corresponding to illumination modes. A pixel array of the reflective SLM and reflects a portion of the sub-beam transmitted by the IMS back to the IMS and PBS. The PBS, IMS, SLM collectively generates a complex amplitude or intensity spatial profile of the transmitted sub-beam.