SummaryIn order to better preserve phospholipids (PLs)‐type polyunsaturated fatty acids (PUFAs) and astaxanthin (ASTA), Antarctic krill oil (AKO) undergoes only limited refining steps, which results in the presence of metal ions. This study aims to establish a metal ion removal method for AKO by using adsorbents and investigate the effects of the metal ion removal process on nutritional composition, oxidation state and colour of AKO, as well as the effects of metal oil removal of AKO on its nutrition composition, oxidation stability and colour stability upon accelerated storage. Among the three types of adsorbents including silica gel, diatomaceous earth, and attapulgite soil, the last one showed the best comprehensive removal effects. After optimising the removal conditions, attapulgite soil achieved the removal rates of 92.5%, 90.0%, and 86.4%, respectively, for iron ions, magnesium ions and calcium ions. Compared to the fresh AKO, the processed AKO had no significant differences in peroxide value (POV), thiobarbituric acid reactive substances (TBARS), and total oxidation value (TOTOX), as well as PUFA content and lipid class composition, indicating that the metal ion removal process would not cause significant lipid oxidation. Moreover, the processed AKO looks brighter and more transparent, and had higher detection values in L*, a*, and b* but lower UV‐vis absorption at 295 nm (A295) and 420 nm (A420). This indicated that the metal ion removal process improved the colour quality. After accelerated storage at 60 °C for 8 days, the processed AKO sample had significantly lower values in POV, TBARS, and TOTOX, but significant higher PUFA content than the fresh AKO group. Moreover, the processed AKO sample had the higher values of L*, a*, and b*, as well as A470 and A495, but the lower values of A295 and A420. The above results indicate that the removal of metal ions significantly improved the stabilities of oxidation and colour of AKO.