Effects of natural catalysts, isothiocyanates and polysulfides, on Z-isomerization and decomposition of (all-E)carotenoids (lycopene, beta-carotene, and astaxanthin) after heat treatment were investigated. When isothiocyanates were added to (all-E)-carotenoid solutions and heated, Z-isomerization and decomposition of carotenoids were enhanced and the degree differed depending on the isothiocyanate type. Interestingly, when polysulfides were applied in the same manner, in addition to promoting the Z-isomerization reaction, they markedly improved the thermal stability of carotenoids. Successively, we investigated the reaction characteristics of allyl isothiocyanate (AITC) and diallyl disulfide (DADS) using (all-E)-lycopene; that is, effects of the amount added, solvent used, and reaction temperature and time, as well as the combination use on Z-isomerization and decomposition of lycopene, were investigated. With increases in the amount added and reaction temperature and time, Z-isomerization of lycopene was promoted for both catalysts. The high-temperature treatment tests clearly showed that AITC induced thermal decomposition of lycopene, whereas DADS improved the lycopene stability. Moreover, the simultaneous use of AITC and DADS resulted in a synergetic effect on the Z-isomerization efficiency.