Abstract: Amphioxus is a valuable marine organism for studying the animal evolution with significant scientific research value. The economic exploitation of amphioxus in Xiamen waters are historically significant. In 1991 Xiamen Amphioxus Natural Reserve was set up. In this study, through an examination of the resources and distribution patterns of amphioxus in Xiamen waters across different time periods, we observed a general decline in overall resource abundance. Specifically, significant changes were noted in the spatial and temporal distributions in Liuwudian waters, while distributions in Qianpu and Nanxian-Shibaxian waters remained relatively stable. Additionally, sporadic occurrences were found in the sea area surrounding Xiaodeng Island. In different historical periods, various marine development and utilization activities, such as land reclamations, sea sand mining operations, mariculture practices and over fishing have significantly impacted the resources of amphioxus and its distribution patterns in Xiamen waters. We present a comprehensive analysis of the existing theoretical and practical research on stock enhancement and substrate environment restoration for amphioxus, focusing on population and habitat restoration. Additionally, we present the development of an assessment index system for amphioxus population restoration and habitat rehabilitation, with resource quantity and habitat area as the core indicators. In the future, a more comprehensive and systematic conservation and restoration effort can be conducted by establishing a systematic and effective assessment system based on expanded survey scope and addressing the environmental requirements of amphioxus in its various life stages.