The effects of some sulfur-containing compounds on the isomerization and degradation of lycopene, phytofluene, and phytoene under different thermal treatment conditions were studied in detail. Isothiocyanates such as allyl isothiocyanate (AITC) and polysulfides like dimethyl trisulfide (DMTS) had the effect on the configuration of PTF (phytofluene), PT (phytoene), and lycopene. The proportion of their naturally occurring Z-isomers (Z1,2-PTF and 15-Z-PT) decreased and transformed into other isomers including all-trans configuration, while Z-lycopene increased significantly after thermal treatment, especially for 5-Z-lycopene. The results showed that increase in heating temperature, time, and the concentration of DMTS and AITC could promote the isomerization reaction effectively to some extent. In addition, 15-Z-PT and the newly formed Z4-PTF were the predominant isomers in tomato at the equilibrium. Unlike the lycopene, which degraded significantly during heat treatment, the isomers of PTF and PT were stable enough to resist decomposition. Moreover, the isomerization of three carotenoids was enhanced, and the bioaccessibility of lycopene increased significantly with the addition of shii-take mushroom containing sulfur compounds, while there was no positive effect observed in that of PTF and PT.