Ionic liquids (ILs) have arisen as alternatives to organic solvents and been used in natural pigment extraction in recent decades. However, the solubility and stability of carotenoids in phosphonium- and ammonium-based ILs are insufficiently explored. In this work, the physicochemical properties of the ILs, and the dissolution behavior and storage stability of three carotenoids (astaxanthin, β-carotene, and lutein) in the IL aqueous solution were investigated. The results showed that the solubility of the carotenoids in the acidic IL solution is higher than that in the alkaline IL solution, and the optimal pH is about 6. The solubility of astaxanthin (40 mg/100 g), β-carotene (105 mg/100 g), and lutein (5250 mg/100 g) was the highest in tributyloctylphosphonium chloride ([P4448]Cl) due to the van der Waals forces with [P4448]+ and hydrogen bonding with Cl−. A high temperature was beneficial to improve the solubility, but it can reduce the storage stability. Water has no significant effect on the carotenoid stability, but a high water content decreases the carotenoid solubility. A IL water content of 10–20%, an extraction temperature of 338.15 K, and a storage temperature of less than 298.15 K are beneficial for reducing the IL viscosity, improving carotenoid solubility, and maintaining good stability. Moreover, a linear correlation was found between the color parameters and carotenoid contents. This study provides some guidance for screening suitable solvents for carotenoid extraction and storage.