Collagen casing is an edible film, which is widely used in the industrial production of sausages. However, the detailed changes in the collagen fibers, from the raw material to the final collagen film, have rarely been reported. In this research, the changes in the collagen fibers during the manufacturing process, including the fiber arrangement, the triple-helix structure and the thermal stability, were investigated using scanning electron microscopy (SEM), thermogravimetric analysis (TGA), X-ray diffraction (XRD), differential scanning calorimetry (DSC) and Fourier-transform infrared (FTIR) spectroscopy. The relationship between the structure stability and the arrangement of the collagen fibers was also discussed. According to the SEM, XRD, TGA, DSC and FTIR results, the collagen fibers were depolymerized during the acid swelling and became uniformly aligned after the homogenization process. Degassing had no obvious effect on the triple-helix structure. Alkaline neutralization with ammonia destroyed the triple-helix structure, which could be partly reversed through the washing and soaking processes. During the final drying step, the depolymerized triple helix of the collagen fibers recombined to form new structures that showed decreased thermal stability. This study expands our knowledge about the behavior of collagen fibers during the industrial process of producing collagen biobased casings.