A new amine-shielded cross-linking method of the chitosan hydrogel beads (CHBs) was investigated to improve the metal adsorption performance of the cross-linked beads. The CHBs were reacted with formaldehyde before the beads were cross-linked with EGDE, and, finally, the amine groups of cross-linked CHBs were released by HCl treatment. Fourier transform infrared spectroscopy and X-ray photoelectron spectroscopy clearly showed that most of the amine groups in chitosan were converted to the -N=CH2 groups after the formaldehyde treatment and they were not involved in the cross-linking reaction with EGDE, and the HCl treatment after the cross-linking reaction effectively released these shielded nitrogen atoms into the form of the primary amine again. Copper ion adsorption experiments confirmed that the CHBs crosslinked with the new method had significantly greater adsorption capacities than the beads crosslinked directly with EGDE. Mechanism study revealed that the increased adsorption performance was attributed to the large number of primary amine groups available on the surfaces of the cross-linked beads from the new cross-linking method.