Astaxanthin is a high-value natural antioxidant, and can be accumulated in Microcystis aeruginosa. To enhance astaxanthin accumulation in the microalgae by using salt stress, the cell growth, photosynthetic abilities, reactive oxygen species (ROS) levels, astaxanthin and its precursor content, and gene expression were investigated under NaCl and KCl stresses. The two salt stresses inhibited the cell growth by lowering photosynthetic abilities and raising ROS levels. During the 6-day treatment, the two salt stresses improved the levels of astaxanthin, precursors (β-carotene and zeaxanthin) and carotenoids, which might be caused by the raised ROS up-regulating expression of 7 related genes. At the same concentration, KCl stress showed stronger inducing effect on astaxanthin and its precursor production than NaCl stress, due to higher expression of related genes. Therefore, NaCl and KCl stresses have obvious ion differences on astaxanthin accumulation, of which KCl stress is more suitable for the high-value antioxidant production from microalgae.