An experimental method was developed in this work to study the PET fibers by synchrotron small-angle X-ray scattering (SAXS). Compared with the traditional measurement in air, the new method measured in the glycerin is helpful to eliminate edge scattering arising from the fiber edge. The results showed that intensity from edge scattering is so high as to cover the microstructure information. PET fiber with a diameter of 25 μm was measured by the new experimental method, and a lobed shape can be seen clearly on the meridian which didn't emerge in traditional measurement. The SAXS data were evaluated to extract parameters of lamellar structure and microvoids. In addition, the effect of fiber diameter on edge scattering was also investigated.