The invention discloses a chromium-based functional nucleic acid sensor and an application thereof in the technical field of metal ion detection. The sensor comprises a molecule recognition element, asignal amplification element and a signal conversion element, wherein the molecule recognition element comprises chromium ion deoxyribozyme consisting of a substrate chain and an enzyme chain; the signal amplification element comprises an isothermal amplification system and hemin, and the isothermal amplification system comprises an amplification template; the signal conversion element comprisesa color developing agent. The sensor is based on the chromium ion deoxyribozyme, an isothermal index amplification reaction and a G-quadruplex liquid phase sensing technology, is convenient, quick, high in sensitivity, high in specificity and resistant to high salinity in chromium ion detection and can be used in field detection of chromium ions in the environment.