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Docosahexaenoic acid (DHA) is an n-3 polyunsaturated fatty acid that is essential for human nutrition. Currently, DHA is commonly produced using Aurantiochytrium, and omics technologies are widely used to investigate the mechanism underlying high DHA production in Aurantiochytrium, providing a foundation for genetic modification of Aurantiochytrium and control of the fermentation process. In this article, the history and major research directions of DHA production by Aurantiochytrium are summarized, and the application of omics technology in Aurantiochytrium is reviewed. It also summarizes recent progress in the application of genomics, transcriptomics, proteomics, metabolomics and multi-omics approaches as well as mathematical models based on omics data to reveal the mechanism underlying high DHA production in Aurantiochytrium. This review concludes with a discussion of future prospects for the development and application of omics technology.