The main objective of this study was to allocate and evaluate the most optimum condition to prepare the chitosan and chitosan nanoparticles that will, subsequently, give the best physicochemical characterization regarding the nanoparticles' size and surface morphology. Chitosan from the exoskeleton wastes of Procambarus clarkii with degree of deacetylation 87% was extracted. Viscometry indicated that the obtained chitosan had a low molecular weight that can be useful in many applications. Chitosan nanoparticles were prepared by using different concentrations of chitosan and the polyanion sodium tripolyphosphate (TPP). For the determination of the optimum condition for the prepared chitosan nanoparticles, three different ratios of chitosan to the polyanion TPP were used, 1:1, 3:1, and 1:3. A novel nanoparticle system composed of low molecular weight chitosan was successfully prepared by the ionotropic gelation technique under an aqueous-based condition. The physicochemical characteristics of chitosan and chitosan nanoparticles were elucidated by Fourier-transform IR spectroscopy, nuclear magnetic resonance spectroscopy, elemental analysis, scanning electron microscopy, transmission electron microscopy, and zeta potential. The best physicochemical characteristics were obtained by adding chitosan to TPP in a ratio of 1:1. The small particle size and narrow range distribution of the obtained chitosan nanoparticles may increase their chance for easy and efficient manipulation for several applications in various fields. In addition, the obtained positively charged chitosan nanoparticles can be used for the delivery of negatively charged compounds.