Natural astaxanthin has been widely used in the food, cosmetic, and medicine industries due to its exceptional biological activity. Shrimp shell is one of the primary natural biological sources of astaxanthin. However, after astaxanthin recovery, there is still a lot of chitin contained in the residues. In this study, the residue from shrimp (Penaeus vannamei) shells after astaxanthin extraction using ionic liquid (IL) 1-ethyl-3-methyl-imidazolium acetate ([Emim]Ac) was used as a bioadsorbent to remove fluoride from the aqueous solution. The results show the IL extraction conditions, including the solid/liquid ratio, temperature, time, and particle size, all played important roles in the removal of fluoride by the shrimp shell residue. The shrimp shells treated using [Emim]Ac at 100 °C for 2 h exhibited an obvious porous structure, and the porosity showed a positive linear correlation with defluorination (DF, %). Moreover, the adsorption process of fluoride was nonspontaneous and endothermic, which fits well with both the pseudo-second-order and Langmuir models. The maximum adsorption capacity calculated according to the Langmuir model is 3.29 mg/g, which is better than most bioadsorbents. This study provides a low-cost and efficient method for the preparation of adsorbents from shrimp processing waste to remove fluoride from wastewater.