The invention discloses the application of ultra-microporous metal-organic framework materials in isotope separation of hydrogen. The ultra-micro porous metal-organic framework material is SIFSIX-3-Zn, used for the effective separation of hydrogen isotopes at low temperature, and the chemical formula of the SIFSIX-3-Zn is Zn (pyr) 2(SiF6). Application of the ultra-microporous metal-organic framework material in the isotope separation of hydrogen enables the separation and purification of D2, H2 in the hydrogen isotope, and the preparation method of the ultra-microporous metal-organic frameworkmaterial is simple. The material can be synthesized in large volumes, and has the advantages of cheap raw materials and low price, and can be widely applied to the industrial hydrogen isotope separation.