Collagen is a protein material with intriguing mechanical properties — it is highly elastic, shows large fracture strength and plays a crucial role in making Nature’s structural materials tough. Collagen based tissues consist of collagen fibrils, each of which is composed out of a staggered array of ultra-long tropocollagen molecules extending to several hundred nanometers. Albeit the macroscopic properties of collagen based tissues have been studied extensively, less is known about the nanomechanical properties of tropocollagen molecules and collagen fibrils, their elementary building blocks. In particular, the relationship between molecular properties and tissue properties remains a scarcely explored aspect of the science of collagen materials. Results of molecular multi-scale modeling of the nanomechanical properties of the large-strain deformation regime of collagen fibrils under varying cross-link densities are reported in this paper. The results confirm the significance of cross-links in collagen fibrils in improving its mechanical strength. Further, it is found that cross-links influence the nature of its large-deformation and fracture behavior. Cross-link deficient collagen fibrils show a highly dissipative deformation behavior with large yield regimes. Increasing cross-link densities lead to stronger fibrils that display an increasingly brittle deformation character. The simulation results are compared with recent nanomechanical experiments at the scale of tropocollagen molecules and collagen fibrils.