Although the research on the cellulose allomorphs has been progressing for decades, many details especially in a nanoscale still require further exploration. In this article, the crystalline structure and morphology of cellulose III nanocrystals (CNC-III) are investigated after some typical modification routes. The results indicate that the crystalline structure of CNC-III is unsteady. After acetylation, hydrophobic cationization, polymer grafting and surface alkylation, CNC-III keep the original crystalline morphology but the crystallinity (62.8 %) decrease to 31.0 %, 42.5 %, 43.1 % and 43.8 %, respectively. However, after TEMPO-mediated oxidation and hydrophilic cationization, the crystalline structure of CNC-III transforms to the cellulose polymorph I and II, respectively. After modification, the dispersibility and thermal stability of CNC-III samples have been changed. Therefore, this systematic investigation is of great significance for understanding the effect of surface modification on the chemical and crystalline structure of CNC-III, which will provide a reference for future modifications and applications.