For the problem of friction damage in cotton fiber processing, a multi-scale combination of investigation methods is proposed. The surface of damaged cotton fiber is detected by relevant test means with damage features such as dislocations, defects and cracks. The internal pyranose ring and glycosidic bond fail, the crystallinity decreases, and the number of hydrogen bonds decreases. Anisotropy exists in the frictional properties of the microscopic surface of the cotton fiber. The results of molecular dynamics simulation showed that the cellulose main chain failed mainly at the glycosidic bond, and the side chain failed mainly at the hydroxymethyl functional group. Its interchain hydrogen bond O3H…O5 was the least damaged. The cellulose crystal (200) surfaces had poor abrasion resistance, and the frictional properties of each crystal surface were anisotropic. The results of the study provide a theoretical basis for improving friction and wear problems in cotton fiber processing.