Abstract: Amphioxus (lancelets), as a surviving species of Cephalophora subphylum of chordate, is a typical transitional species in the evolution process from invertebrate to vertebrate, and plays an extremely important role in the study of the origin and evolution of vertebrates. In this study, the MaxEnt model was used to analyze the potential habitat and the environmental factors limiting the distribution of Amphioxus within Xiamen State-Level Marine Nature Reserve for Rare Marine Species (here we call it as nature reserve) in Huangcuo area. Results show that the total area of potential suitable habitat is 575.48 hm², accounting for 30.76% of the total area of the nature reserve, the suitable area has a limited extent of only 63.39 hm², exhibiting a fragmented distribution pattern and evident habitat fragmentation. The important environmental factors affecting the amphioxus distribution are the fraction of sand grains (>0.125 mm) of the sediments as well as the water depth. In consideration of the depletion of amphioxus and habitat degradation in Xiamen area, it is imperative to implement long-term monitoring for both the amphioxus population and its habitats. Furthermore, conducting comprehensive assessments of habitat quality and suitability is necessary, as it will provide a scientific foundation for identifying and designating restoration target areas. Such efforts are crucial for safeguarding the amphioxus population and maintaining ecological balance.