Driven by Industry 4.0, digital twin, as a key enabling technology for digital transformation and intelligent upgrade, has attracted growing attention in various fields of agriculture, such as aquaponics factory. Although the digital twin has made formidable progress in theory and application, there are still many doubts and challenges for aquaponics factory. Based on a review of publications related to digital twin, in this contribution, we summarized the connotation of digital twin, including an overview of the research evolution, architecture, and clarification of digital twin and other concepts, such as cyber-physical systems and simulations. Enabling technologies of digital twin are also introduced from a five-dimensional model perspective. On the basis of maintaining a consensus understanding of digital twin, we explored the potential of digital twin in aquaponics without violating the initial vision of digital twin. First, we provided a comprehensive and insightful summary of aquaponics factory and the application of digital twin in agriculture, with the aim of discovering the possibilities and directions for introducing digital twin into aquaponics factory. Then, we dissected in detail practical cases of digital twin related to the production of aquaponics factory, highlighting the added value that digital twin may bring to aquaponics factory, and explored urgent challenges and research directions.