Squid oil is a rich source of ω-3 fatty acids (including EPA and DHA), which are highly beneficial to human health. However, the refining of squid oil is challenging due to its dark color, high acid value, and strong fishy odor. This study investigates enzyme-catalyzed deacidification as an alternative to conventional alkali refining. The aim is to reduce the acid value and optimize the deacidification process. Comparative experiments were carried out using four commercial lipases (Lipozyme 435, Lipozyme TL IM C, Lipozyme RM IM C, and DF Amano IM) and a self-prepared immobilized enzyme (GS “Amano” 250G). Lipozyme 435 showed the highest deacidification efficiency. Subsequently, single-factor experiments and a Box–Behnken design combined with response surface methodology were applied to optimize the enzymatic deacidification process. The optimal conditions were determined to be a reaction time of 6 hours, an ethanol concentration of 19%, and an enzyme loading of 83 PLU/g. Under these conditions, the acid value of the squid oil was reduced from 60.17 mg KOH/g to 2.27 mg KOH/g, corresponding to a deacidification rate of 94.58% and a yield of 73.22%. Notably, this yield represents a significant 51.28% improvement compared to traditional alkali refining. The enzymatic deacidification method offers several advantages over traditional processes, such as simplicity, higher yield, lower energy consumption, and reduced pollution. Additionally, the use of molecular sieves and high-speed homogenization to enhance substrate solubility proved effective in improving deacidification efficiency. Overall, these findings provide valuable technical insights and support for the enzymatic deacidification of high-acid squid oil.