Methods and systems for controlling illumination beam spot size for Transmission, Small-Angle X-ray Scatterometry (T-SAXS) measurements of different sized metrology targets are described herein. An X-ray illumination optics subsystem includes one or more focusing optical elements with object and image planes at fixed locations and one or more illumination apertures or slits that independently control magnification and beam divergence. In a further aspect, the illumination source size and shape is controlled, along with magnification and beam divergence. In this manner, beam divergence and illumination spot size on a specimen are independently controlled, while maintaining constant illumination flux.