Abstract: Antarctic krill oil (AKO) is a valuable marine lipid rich in phospholipids, astaxanthin, and ω-3 PUFAs (EPA, DPA, DHA), with proven blood lipid regulation, cardiovascular protection, antioxidant, and cognitive benefits, making it highly promising for functional foods. However, its industrial use is severely limited by inherent flaws. Unsaturated double bonds in AKO are prone to hydrolysis and oxidation during storage and processing, elevating acid value, peroxide value (POV), and thiobarbituric acid reactive substances (TBARS). This deterioration reduces nutritional value and generates fishy off-flavors from aldehydes, ketones, and alcohols, impairing sensory quality. Additionally, poor water solubility and aqueous matrix compatibility cause aggregation, restricting applications in beverages, dairy, and emulsified foods. Emulsification is an effective modification strategy, with microemulsions and Pickering emulsions as key research focuses. However, systematic studies on AKO quality evolution in different emulsion systems and underlying stabilization mechanisms are still lacking. Here, pure AKO, AKO microemulsion (AKO-ME), and AKO Pickering emulsion (AKO-PE) were stored at 25°C for 16 days to simulate commercial storage conditions. Dynamic changes in physicochemical properties, functional components, and volatile flavors were comprehensively analyzed. Results showed both emulsions significantly inhibited lipid hydrolysis and oxidation. After 16 days, pure AKO showed 85.40%, 328.93%, and 707.64% increases in acid value, POV, and TBARS, respectively, while AKO-PE exhibited the best stability with 33.43%, 96.69%, and 386.09% increases. Emulsification also reduced losses of phospholipids, astaxanthin, and ω-3 PUFAs: astaxanthin retention was 65.27% in pure AKO versus 79.52% in AKO-ME and 78.62% in AKO-PE; total ω-3 PUFAs retention was 79.98%, 83.93%, and 83.58%, respectively. Furthermore, emulsions decreased fishy aldehyde content and increased pleasant alcohols and esters, significantly improving overall flavor quality. This study confirms that microemulsions and Pickering emulsions effectively enhance the storage stability and sensory quality, providing critical theoretical support for its food industry application. Future research should focus on developing natural low-cost emulsifiers, elucidating stabilization mechanisms, expanding food application scope, and establishing industry quality standards to promote the standardized large-scale development of AKO functional foods.