Bombyx mori silk fibroin (B. mori SF) is a promising biopolymer for use in biomedical applications such as tissue engineered grafts and as a load bearing biopolymer with biocompatible and bioresorbable properties. B. mori SF is a hierarchical bio- macro-molecule made up of amino acid (residue) chains consisting of a crystalline phase and an amorphous phase arranged in a specific order. Understanding about the mechanical behavior of B. mori SF at multiple length scales is of importance when developing tissue grafts, which requires a deeper understanding of the mechanics of its nanostructure. Four phenomenological models of B. mori SF nanostructures were developed, based on crystalline and amorphous phase connectivity. Tensile loading based mechanical behavior analysis of these models were performed using molecular dynamics (MD) simulations and compared with existing results from literature for selection of best performing model. Elastic modulus of ~7.4GPa and tensile strength of ~340 MPa were obtained for this model. Analysis of results reveals that deformation mechanisms in B. mori SF at nanoscale are a combination of tensile and shear deformations, wherein, the tensile deformation of amorphous region results into excessive extension of B. mori SF, whereas, shear deformation of crystalline region results into a high tensile strength. Overall, this work is instrumental in development of a right computational nanoscale model of SF nanostructure and provides deeper insights into the mechanistic interactions and mechanisms between amorphous and crystalline regions of B. mori SF, which would be useful for further studies of silk based biomaterials.