A well tested multi-scale modelling approach, which was described and formulated in our previous work Ebrahimi et al. (2012), is employed to investigate the elasto-plastic behaviour of the chitosan (Cs) biological polymer embedded with a hydrogenated graphene (Gr–H), and a hydrogenated carbon nanotube (CNT–H). Without any need of a parameter fitting, and the inter-atomic potentials are directly linked into a continuum-based computation, via the Cauchy–Born rule. The continuum point within a finite element (FE) mesh in continuum level is represented by an atomic cluster. The results show that H-coverage and deformation of carbon nanostructures can lead to a drop in tensile modulus of nanocomposites. In addition, we show that, deformation of nanostructures play an important role in mechanical properties of nanocomposites.