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Antarctic krill (Euphausia superba) is one of the important bioresources in Antarctic waters, containing many bioactives (e.g., astaxanthin), which have a highly potential value for commercial exploitation. In this study, the effects of processing methods on the content, structural isomers, and composition of astaxanthins (free astaxanthin and astaxanthin esters) were studied. Three drying methods, comprising freeze-drying, microwave drying, and hot-air drying, were used. Free astaxanthin (Ast), astaxanthin monoesters (AM), and astaxanthin diesters (AD) in boiled krill (control) and dried krill were extracted and analyzed using high-resolution mass spectrometry with ultraviolet detection. After the three processes, total astaxanthin loss ranged from 8.6 to 64.9%, and the AM and AD contents ranged from 78.3 to 16.6 and 168.7 to 90.5 μg/g, respectively. Compared to other kinds of astaxanthin esters, astaxanthin esters, which linked to eicosapentaenoic acid and docosahexaenoic acid, as well as the Ast, were more easily degraded, and AM was more susceptible to degradation than AD. All-E-astaxanthin easily transformed to the 13Z-astaxanthin than to the 9Z-astaxanthin during the drying process, but the proportions of optical isomers changed due to drying by no more than 5%. The results suggested that freeze-drying, low-power microwave drying (≤1 kW), and low-temperature hot-air drying (≤60 °C) are optimal drying methods for ensuring the quality of krill products.