Collagen, one of the major components in the mammalian connective tissues, plays an essential role in many vital physiological processes. Many common diseases, such as fibrosis, overuse injuries, and bone fracture, are associated with collagen arrangement defects. However, the underlying mechanism of collagen arrangement defects remains elusive. In this study, we applied infrared scattering-type scanning near-field optical microscopy to study collagen fibrils’ structural properties. Experimentally, we observed two types of collagen fibrils’ arrangement with different periodic characteristics. A crystal sliding model was employed to explain this observation qualitatively. Our results suggest that the collagen dislocation propagates in collagen fibrils, which may shed light on many collagen diseases’ pathogenesis. These findings help to understand the regulation mechanism of hierarchical biological structure.