Preparing strong and flexible atelocollagen-based materials for biomedical applications is still a challenging task. To address this challenge, this study describes the synthesis and characterization of water-soluble polyrotaxanes (PRs) with different coverage ratios and molecular weights of axle polymers, and their potential applications for PR-reinforced atelocollagen threads (PRATs). A novel method was established for the syntheses of PRs with relatively low coverage ratio at the sub-gram scale, in which the aldehyde groups were employed as crosslinking sites for preparing the PRATs via reductive amination. The aldehyde groups were successfully quantified by 1H nuclear magnetic resonance spectroscopy using 1,1-dimethylhydrazine as an aldehyde marker. Fourier-transform infrared and thermogravimetric analysis measurements supported the characterization of the PRs. Interestingly, tensile testing demonstrated that coverage ratio affected the mechanical properties of the PRATs more strongly than molecular weight. The insights obtained in this study would facilitate the development of soft materials based on atelocollagens and PRs.