The invention relates to a preparation method of Z-1,1,1,4,4,4-hexafluoro-2-butene, belonging to the field of chemical synthesis. The method comprises the following steps of taking hexachlorobutadiene (HCBD) as a raw material, performing gas-phase catalytic chlorination-fluoridation separation to obtain 2,3-dichlorohexafluoro-2-butene, performing liquid-phase dechlorination to obtain hexafluoro-2-butyne, and preparing the Z-1,1,1,4,4,4-hexafluoro-2-butene (Z-HFO-1336mzz) by means of performing gas-phase catalytic hydrogenation, wherein three reactions are included totally. The Z-1,1,1,4,4,4-hexafluoro-2-butene with high selectivity is obtained by means of performing catalytic hydrogenation by adopting the hexafluoro-2-butyne, and meanwhile the product is easily separated from side products and the raw material. The method disclosed by the invention has the advantages that the original raw material is easily obtained, the activity of a catalyst is high, the service life of the catalyst is long, the raw material can be recycled, and the standard of zero emissions is reached.