The chemical structure, thermal denaturation and nanostructure of collagen, obtained from a cation-exchange separation of the mantle, fins and tentacles of jumbo squid (Dosidicus gigas), were comparatively studied. The main idea of this work, was to provide an in-depth understanding of the interdependence between pyridinoline (Pyr) content, helix chemical structure and nanostructure of squid collagen with squid tissue firmness. The tentacles required more shear force and its collagen presented the higher temperature and enthalpy of transition, than the mantle and fins. The tentacle firmness may be explained by the relatively higher imino amino acid content, proline and lysine hydroxylation degrees and Pyr content of its collagen. Moreover, among the regions studied, the collagen from the tentacles had a more intense β band chain. Also, the Fourier transform infrared analysis and Raman spectra, implied that the collagen in the tentacles, was more intermolecularly ordered than the mantle and fins. Consistent with these results, a comparative evaluation of the surface morphology of the three regions, with atomic force microscopy, suggested a more ordered collagen structure in the tentacles (lower roughness values). Based on the above, collagen from tentacles has a higher degree of molecular order that sustains a higher muscle firmness compared to that of other anatomical regions.