Benzoxazines have attracted wide attention from academics all over the world because of their unique properties. However, most of the production and preparation of benzoxazine resins depends on petroleum resources now, especially bisphenol A-based benzoxazine. Therefore, owing to the environmental impacts, the development of bio-based benzoxazines is gaining more and more interest to substitute petroleum-based benzoxazines. Similar to petroleum-based benzoxazines, most of bio-based benzoxazines suffer from flammability. Thus, it is necessary to endow bio-based benzoxazines with outstanding flame retardancy. The purpose of this review is to summarize the latest advance in flame retardant bio-based benzoxazines. First, three methods of the synthesis of bio-based benzoxazines are introduced briefly. Furthermore, the curing mechanism of benzoxazine and the effect of branched chains on the curing behavior are also discussed and summarized. Subsequently, this review focuses on fully bio-based benzoxazines, partly bio-based benzoxazines, and bio-based benzoxazine composite materials in terms of flame retardancy as well as thermal stability and some other special properties. Finally, we give a brief comment on the challenges and prospects of the future development of flame retardant bio-based benzoxazines.