The production of high-performance carbon fibers relies heavily on the structural transformations of polyacrylonitrile (PAN) fiber during processing. In this article differential scanning calorimetry (DSC), synchrotron small-angle X-ray scattering (SAXS), and synchrotron wide-angle X-ray diffraction (WAXD) were used to study the changes of the thermal properties, voids and crystal structure of the PAN precursor fibers on industrial lines during the continuous processing stages, i.e., after the treatment in the coagulation bath, after stretching in boiling water and after stretching in high-temperature steam. The findings of this study suggest that after boiling water stretching the molecular chain motion of the PAN precursor fiber weaken, resulting in the expansion of the voids. After high-temperature steam stretching the voids became elliptical and oriented in the stretching direction. Although the boiling water stretching process partially damaged the (100) crystal planes of the PAN precursor fibers, it does not hinder their overall crystalline structure. The high stretching ratio primarily affected the orientation of the molecular chains. This orientation, even in the context of partial crystal plane disruption, further promoted the crystallization of the (100) crystal planes in the fibers. These experiments explored the correlation between the processing technology and fiber structure transformation of PAN-based carbon fibers, resulting in producing a guide for the preparation of high-performance carbon fibers with fewer defects.