Chitosan is biocompatible polymer has a great commercial interest because it can be processed in a sort of devices varying in shape and size, such as membranes, gels and nanoparticles. Mostly, the cell’s attachment and proliferation are very positive on nanostructurated materials with a three-dimensional formation. An irreversible network can be produced by covalently binding the polymer to the cross-linker molecules. Chitosan nanoparticles were prepared using glutaraldehyde as cross-linker. This crosss-liker mostly reacts with chitosan amino groups. In order to control and understand the physical characteristics of chitosan nanoparticle, in this work is showed the molecular behavior of chitosan/glutaraldehyde from the viewpoint of molecular interactions base in a series of molecular dynamics (MD) computer simulation. The results indicated the conformations of both molecules, which had a significant influence on the molecular association. The chitosan chains were uniformly distributed presenting a high flexibility and preference for the relaxed two-fold helix. This was due to the various associations such as intramolecular chitosan interactions –O-H···O-C-. While the chitosan-glutaraldehyde associations were due to the positive net charge density of hydrogens in the chitosan plus - H2N···C=O associations. In solid state chitosan nano and microparticles were analyzed by scanning electron microscopy (SEM). According to the micrographs results, the nanoparticles presented a monomorphism with piles of particles arranged in linear order which was consistent with the conformations determined by simulation.