Collagen, the dominating material in the extracellular matrix, provides the strength, elasticity and mechanical stability to the organisms. The mechanical property of collagen is mainly dominated by its surrounding environments. However, the variation and origin of the mechanics of collagen fibril under different concentrations of calcium ions (χCa) remains unknown. By using the atomic force microscopy based nanoindentation, the mechanics and structure of individual type II collagen fibril were first investigated under different χCa in this study. The results demonstrate that both of the mechanical and structural properties of the collagen fibril show a prominent dependence on χCa. The mechanism of χCa-dependence of the collagen fibril was attributed to the chelation between collagen molecules and the calcium ions. Given the role of calcium in the pathology of osteoarthritis, the current study may cast new light on the understanding of osteoarthritis and other soft tissue hardening related diseases in the future.