Chitosan (CS)/tripolyphosphate (TPP) nanoparticles were synthesized using the ionic gelation method based on the mass ratio and volume ratio between CS and TPP and then subsequently characterized using XRD, FT-IR, and SEM. The interaction between the metal ions Co(II), Cr(III), and Cu(II) on CS and 2CS/TPP was simulated using molecular dynamics (MD), and the findings were compared with the experimental data. CS/ TPP nanoparticles were more favorable than using pure chitosan at a % removal efficiency of 91.47, 89.11, and 78.11 for Cu(II), Cr(III), and Co(II), respectively. The binding energy between 2CS/TPP and the metals was more favorable than that for CS at −214.95, −106.87, and −58.11 kcal/mol for Cr(III), Co(II), and Cu(II), respectively. The CS/TPP nanoparticles greatly affect metal adsorption and are therefore considered materials for wastewater treatment.