Chitosan, including native, N- alkyl (AlkCs), and nanoparticles chitosan (CsNPs), were prepared and characterized. Average size and hydrodynamic diameter of nanoparticles were determined at 126 nm and 240 nm with a polydispersity index (PDI) of 0.154 and zeta potential of 30 mV, respectively. Crystallinity index for Cs, AlkCs, and CsNPs was calculated as 57.85, 30.24, and 24.85, respectively. Minimum concentration of growth inhibition (125.78 µg/ml) and lethality (100 µg/ml) was observed for CsNPs (P < 0.05). CsNPs and AlkCs showed the highest diameter of the growth inhibition zone at 1250 μg/mL concentration, respectively (P < 0.05). Membrane permeability test, the highest absorption of ortho-nitrophenol was observed after 90 min with 0.11 nm. The most significant decrease in absorption in chitosan was observed at the end of 120 min. DAPI (4′,6-Diamidino-2-Phenylindole) staining test showed higher cell death of bacteria treated with AlkCs and CsNPs. Images obtained from atomic force microscopy (AFM) showed a change in the morphology of the treated cells compared to the spherical and clustered control cells. A significant increase in the expression of vraS, vraR, lytM, lrgA and lrgB genes was observed as a result of induction of S. aureus cell wall by Cs, AlkCs and CsNPs, d.