•Cellulose nanocrystals (CNs) with different polymorphs (I and II) were obtained.•CNs with different sizes and shapes (cilindrical and circular) were obtained.•CNs composed of cellulose II had lower DP values than CNs composed of cellulose I.•CNs extracted using H2SO4 were less thermally stable than those extracted using HCl.•The type of polymorph and acid employed affected the thermal degradation kinetics. Cellulose nanocrystals (CNs) were extracted from different sources by acid hydrolysis using H2SO4 and HCl. The thermal decomposition of resulting CNs was studied by thermogravimetric analysis (TGA). The kinetic parameters were determined using the Flynn–Wall–Ozawa (FWO) and Kissinger methods. CNs were also characterized by X-ray diffraction (XRD), Atomic Force Microscopy (AFM), elemental analysis (EA), Zeta Potential (ZP) and degree of polymerization (DP). The results of the XRD analysis showed different profiles, making it possible to differentiate cellulose I from cellulose II. The results obtained by the FWO method showed that cellulose II CNs had an increased activation energy (Ea) with conversion (α), while in CNs of cellulose I the Ea remained constant or decreased slightly. This difference between Ea values for the thermal decomposition of CNs was mainly attributed to different crystalline arrangements of cellulose I and cellulose II, and to the type of acid employed.