Transformation of allylic alcohols to corresponding saturated carbonyl compounds is one of the important reactions for industrial processes. Lately, Au-supported catalysts exhibit the catalytic activity for the isomerization of allylic alcohols to saturated aldehydes. However, the detail catalytic mechanism of this reaction was not elucidated in detail. Thus, theoretical calculations were carried out for the isomerization of 2-hexen-1-ol over isolated Au6 cluster in order to elucidate the reaction over Au catalysts. From these calculation results, it was found that the rate determining step of the reaction process was the hydrogen elimination from OH group of allylic alcohol, and the substrate was converted to 1-hexen-1-ol on Au6 cluster. Finally, it was also confirmed that 1-hexen-1-ol was converted to the corresponding aldehyde, and its activation barrier was much smaller than that of the deprotonation from OH group of allylic alcohol.