Fluorine is one of the essential trace elements for human body, which is essential for calcification process in living organisms. In the paper, a “off–on” fluorescence sensor for fluorine ion based on aluminium ion and boric acid codoped carbon dots was synthesized and characterized. According to fluorescence analysis, the water-soluble sensor exhibited highly selective and sensitive for fluorine ion. In sensing process, F- could bind to Al3+ after the addition of fluorine ion, which resulted in the decomposition of Al-BA-CDs system, then intense yellow fluorescence signal appeared. Moreover, the fluorescence sensor exhibited low detecting limit (5.0 nanomolar level) by fluorescence titration spectrum. In addition, according to evaluate the fluorescence sensing properties of F- in HepG2 cell and zebra fish, this job greatly extended the use of F- sensor from aluminium ion and boric acid codoped carbon dots in organism. The work also provided an interesting idea for fabricating water-soluble fluorescence sensor for F-.