Collagen is an abundant structural biopolymer in mammal vertebrates, providing structural support as well as mechanical integrity for connective tissues such as bone, ligament, and tendon. The mechanical behaviours of these tissues are determined by the nanomechanics of their structures at different hierarchies and the role of collagen structures in the extracellular matrix. Some studies revealed that there is significant microstructural difference in the longitudinal direction of the collagen fibril, which challenges the conventional rod-like assumption prevalently adopted in the existing studies. Motivated by this discrepancy, in this study, we investigated the longitudinal heterogeneous nanomechanical properties of type I collagen molecule to probe the origin of the longitudinal heterogeneity of the collagen fibril at the molecular level. A full length type I collagen molecule structure was built based on the experimentally calibrated nano-structure. Then, a suitable strain rate was determined for stretching the three intact ‘gap’ regions and three intact ‘overlap’ regions of the collagen molecule. Further, the nanomechanical properties of the six collagen molecule segments were characterized by performing steered molecular dynamics simulations, using the obtained suitable strain rate in modelling. The results indicate that this computational model can be used to capture the mechanical behaviour of the collagen molecule under physiological stress conditions. Moreover, the ‘gap’ regions show a lower stiffness and undergo a slightly lager strain in the unwinding process, compared to the ‘overlap’ regions of the collagen molecule. This investigation provides insights into the origin of the longitudinal heterogeneity of collagen fibrils at the molecular level, and suggests that it is of significant importance to consider the longitudinal heterogeneous mechanical properties of the collagen molecule in the development of coarse-grained models of collagen-related tissues.