A novel hexagonal fluorinated aluminophosphate molecular sieve has been prepared ionothermally using 1-ethyl-3-methylimidazolium bromide as solvent and template provider in the presence of HF. The resulting fluorinated aluminophosphate molecular sieve is hexagonal nanoflakes with a thickness of about 170nm and has the single-crystal property. Further comparative experiments show that fluoride ions have a strong effect on the morphology and framework of the samples.