In this study, the cross-linked chitosan-polyphosphate-epichlorohydrin (CCPE) beads were prepared by cross-linking chitosan with both polyphosphate and epichlorohydrin and used as bioadsorbent for the removal of Pb(II) and Cu(II) ions from aqueous solutions. The effects of the dosage of CCPE beads, solution pH, initial metal ion concentration, contact time, and temperature were investigated. Then, three important factors were selected to optimize the removal processes by the orthogonal test. The results show that CCPE beads can effectively remove the Pb(II) and Cu(II) ions from aqueous solutions, and the maximum percentage removals for Pb(II) and Cu(II) ions are 99.7% and 91.2%, respectively. The data show also that the removal processes for both Pb(II) and Cu(II) ions fit best the pseudo-second order kinetic model. Moreover, the decrease of the adsorption ability of CCPE beads is less than 10% after reuse for 9 times, which suggests that CCPE beads have good reusability.