Chitosan-based hydrogel beads were prepared through neutralization with an alkali gelation process, whereas pristine hydrogel capsules with a core shell membrane structure were synthesized through an anionic surfactant gelation process. The anionic surfactant (sodium dodecyl sulfate; SDS) in the capsules was completely extracted through a green exchange with an (NaOH) alkali solution. The extracted surfactant solution can be continuously reused for synthesizing hydrogel capsules. The effects of alkali treatment on the changes in the morphology, surface chemistry, and adsorption capacity of the capsules were investigated. The results indicated that the NaOH-treated capsules exhibited similar chemical compositions but dissimilar structures to the pristine hydrogel capsules. Optimal synthesis conditions of the green capsules (SN5) were obtained at 5 g/L of SDS gelation and 0.02 N NaOH. Moreover, the mechanical stability of hydrogel capsules was insignificantly changed by the alkali treatment as evidenced by their mass loss under ultrasonication. The alkali treatment process can remarkably enhance the adsorption rate and capacity of Congo red dye onto the capsules. The treated capsules (2592 mg/g) exhibited an excellent adsorption capacity compared to the pristine hydrogel capsules (563 mg/g) and beads (183 mg/g) because of the rearrangement of polymeric networks after the alkali treatment process. The alkali treatment process can significantly improve the adsorption capacity of capsules and completely remove the SDS surfactant in capsules. Therefore, NaOH-treated hydrogel capsules can serve as a biocompatible and green adsorbent with excellent adsorption capacity.