As a highly crystalline and renewable natural polymer nanomaterial, chitin nanocrystals (ChNCs) have attracted intense interest in the biomedical field. The structure of a ChNC is composed of an acetylglucosamine unit containing two hydroxyl groups and an acetyl group. The acetyl group can be converted to the active amino group through deacetylation, which is under the condition of maintaining the rod-like morphology and high crystalline property and is beneficial for the following modification and potential application. We investigated the relationship between different treatments and varied crystallinities of the modified ChNC, which obtained surface amino groups and aldehyde groups and retained high crystallinity. The natural biomolecules were covalently immobilized on the surface of the ChNC. The etherification was performed based on the hydroxyl groups. Based on the amino groups and the aldehyde groups, the carboxyamine and Knoevenagel condensation reactions were realized on ChNCs. Finally, natural biomolecule-modified ChNCs showed no or low cytotoxicity, antibacterial properties, and high antioxidant properties, which extended their potential biomedical applications.