Astaxanthin, which is an important metabolite with anti-oxidative property, has been discovered in some fish, shrimp, and microorganisms. Owing to the great advantages of microalgae-based astaxanthin in the aspects of sustainability and safety, microalgal astaxanthin is emerging into the limelight. In the past years, researchers isolated a couple of microalgal species and explored the synthesis pathways of astaxanthin in algal cells. Also, specific culture conditions, such as nitrogen deficiency, high-intensity illumination, and supply of glucose, salt or trace elements, promoting the accumulation of astaxanthin in microalgal cells have been intensively studied. The main goal of this paper is to review the progresses in the production of microalgal astaxanthin and promote the wide use of microagal astaxanthin in aquaculture. In this regard, we summarized the studies on algal strains screening, synthetic mechanisms of microalgal astaxanthin, microalgae cultivation models, and fish-rearing with astaxanthin supplement. Based on the literature review, we discussed the challenges threatening the production and application of microalgal astaxanthin and pointed out the prospects of microalgal astaxanthin in the future. This work will provide a deep understanding of microalgal astaxanthin and its application in aquaculture.