In this study, cellulose nanocrystals with cellulose crystal structure I (CNCs I) and with coexisting cellulose crystalline structures I and II (CNCs I-II) were isolated from pine cellulose using acid hydrolysis with H2SO4. It was possible to obtain CNCs with different morphologies, crystallinities and crystalline structures adjusting only the reaction conditions. The thermal stability is directly related to the crystalline structure and the crystallinity. It was observed that CNCs composed mainly of CNC II have an initial degradation temperature higher than the CNCs I when comparing samples with similar crystallinity. The kinetic results allow us to conclude that activation energy (E-a) not only depends on the crystalline structure and crystallinity of the CNCs but may also be related to the presence of sulfate groups. Understanding the influence of crystallinity and crystalline structure on the thermal stability of CNCs can direct the studies of future applications for these materials.