Bone is a living tissue made up of organic proteins, inorganic minerals, and water. The organic component of bone (mainly made up of Type‐I collagen) provides flexibility and tensile strength. Solid‐state nuclear magnetic resonance (ssNMR) is one of the few techniques that can provide atomic‐level structural insights of such biomaterials in their native state. In the present article, we employed the variable contact time cross‐polarization (1H‐13C CP) kinetics experiments to study the hydration‐dependent atomic‐level structural changes in the bone extracellular matrix (ECM). The natural abundant 13C CP intensity of the bone ECM is measured by varying CP contact time and best fitted to the nonclassical kinetic model. Different relaxation parameters were measured by the best‐fit equation corresponding to the different hydration conditions of the bone ECM. The associated changes in the measured parameters due to varying levels of hydration observed at different sites of collagen protein have provided its structural arrangements and interaction with water molecules in bone ECM. Overall, the present study reveals a better understanding of the kinetics of the organic part inside the bone ECM that will help in comprehending the disease‐associated pathways.