Liposomes are regarded as the ideal nanocarrier for concurrent or separate delivery of nutraceuticals in the food industries. Precise control of the structural stability is essential for the processing, storage, and nutrition delivery of liposomes. Astaxanthin was found to significantly affect the membrane stability of liposomes by inserting into the phospholipid bilayers in a similar way to cholesterol. Compared with cholesterol, astaxanthin could significantly improve the phase transition temperature, membrane fluidity, and membrane compactness of liposomes. Additionally, the membrane stability was well modulated by controlling the distribution patterns of astaxanthin (monomers, H- and J-aggregates) in bilayers. For instance, astaxanthin H-aggregates could endow the liposomal membrane with highest rigidity and compactness. Additionally, astaxanthin aggregates, especially J-aggregates could greatly improve storage stability of liposomes, thus providing a novel strategy to regulate and optimize the stability of liposomes for their diversified applications.