A group of CuAPO-5 molecular sieves with trace Cu were successfully synthesized via an ionothermal method and used for fructose dehydration to 5-hydroxymethylfurfural (HMF) in [BMIM]Br ionic liquid. The 0.06-CuAPO-5 sample displayed excellent performance and a HMF yield of 93.8% was obtained, which could be ascribed to the balance between acid strength and mass transfer efficiency. This work demonstrates that the ionothermal synthesized CuAPO-5 molecular sieve was also a good candidate for the efficient production of HMF.