In this study, medical cotton was subjected to acid hydrolysis in sulfuric, hydrochloric and phosphoric acid medium to prepare cellulose nanocrystals (CNC) with different morphologies and polymorphism. Morphology of the prepared CNC samples revealed fiber shaped morphology for sulfuric and hydrochloric acid hydrolyzed samples, whereas, spherical shaped for phosphoric acid hydrolyzed samples. The size of the spherical shaped CNC decreased with the increase of hydrolysis time, from 853 nm for 12 h to 187 nm for 48 h. X-ray Diffraction analysis showed that hydrochloric acid hydrolyzed CNC is cellulose I (CI), phosphoric acid hydrolyzed CNC is cellulose II (CII) and sulfuric acid hydrolyzed CNC contain both CI and CII. The crystallinity of sulfuric and hydrochloric acid hydrolysis samples was 91%, whereas, the crystallinity of phosphoric acid hydrolysis samples was between 43 and 60% depending on hydrolysis time. Thermal properties were also affected by the hydrolysis medium. Thus cellulose nanocrystals were prepared with different morphologies and physical characteristics through a facile method.