Isochrysis galbanais considered an ideal bait for functional foods and nutraceuticals of humans because of its highfucoxanthin(Fx) content. However, multi-omics analysis of the regulatory networks for Fx biosynthesis inI.galbanahas not been reported. In this study, we report a high-quality genome assembly ofI.galbanaLG007, which has a genome size of 92.73 Mb, with a contig N50 of 6.99 Mb and 14,900 protein-coding genes. Phylogenetic analysis confirmed the monophyly of Haptophyta, withI.galbanasister toEmiliania huxleyiandChrysochromulina tobinii.Evolutionary analysis revealed an estimated divergence time betweenI.galbanaandE. huxleyiof ∼ 133 million years ago. Gene family analysis indicated that lipid metabolism-related genes exhibited significant expansion, includingIgPLMT,IgOAR1, andIgDEGS1.Metabolomeanalysis showed that the content of carotenoids inI.galbanacultured under green light for 7 days was higher than that under white light, and β-carotene was the main carotenoid, accounting for 79.09% of the total carotenoids. Comprehensive multi-omics analysis revealed that the content of β-carotene, antheraxanthin, zeaxanthin, and Fx was increased by green light induction, which was significantly correlated with the expression ofIgMYB98,IgZDS,IgPDS,IgLHCX2,IgZEP,IgLCYb, andIgNSY. These findings contribute to the understanding of Fx biosynthesis and its regulation, providing a valuable reference for food and pharmaceutical applications.