Cellulose nanocrystals (CNCs) are attractive materials due to their renewable nature, high surface-to-volume ratio, crystallinity, biodegradability, anisotropic performance, or available hydroxyl groups. However, their source and obtaining pathway determine their subsequent performance. This work evaluates cellulose nanocrystals (CNCs) obtained from four different eucalyptus species by acid hydrolysis, i.e., E. benthamii, E. globulus, E. smithii, and the hybrid En × Eg. During preparation, CNCs incorporated sulphate groups to their structures, which highlighted dissimilar reactivities, as given by the calculated sulphate index (0.21, 0.97, 0.73 and 0.85, respectively). Although the impact of the incorporation of sulphate groups on the crystalline structure was committed, changes in the hydrophilicity and water retention ability or thermal stability were observed. These effects were also corroborated by the apparent activation energy during thermal decomposition obtained through kinetic analysis. Low-sulphated CNCs (E. benthamii) involved hints of a more crystalline structure along with less water retention ability, higher thermal stability, and greater average apparent activation energy (233 kJ·mol−1) during decomposition. Conversely, the high-sulphated species (E. globulus) involved higher reactivity during preparation that endorsed a little greater water retention ability and lower thermal stability, with subsequently less average apparent activation energy (185 kJ·mol−1). The E. smithii (212 kJ·mol−1) and En × Eg (196 kJ·mol−1) showed an intermediate behavior according to their sulphate index.