The purpose of this work was to investigate the differences in the anti-oxidative stress and anti-inflammatory effects between all-E (trans)-lutein and its 9Z (cis)- and 13Z-isomers using the human intestinal Caco-2 cell model. I–TiO2 catalyst was used to isomerize all-E-lutein to obtain 9Z-lutein and 13Z-lutein. In anti-oxidative stress studies, all three lutein isoforms could significantly reduce H2O2-induced interleukin-8 (IL-8) and tumor necrosis factor-α (TNF-α) secretion (p < 0.05) by 50% or more at 4 μM. At lower concentration (2 μM), 9Z-lutein and 13Z-lutein showed higher protection against oxidative stress than all-E-lutein by significantly reducing IL-8 secretion by 48% and 40% (p < 0.05), respectively. In addition, three lutein isomers, especially 9Z-lutein could up-regulate the activity of antioxidant enzymes including catalase (CAT), glutathione peroxidase (GPx), glutathione reductase (GR), and the content of endogenous antioxidant glutathione (GSH) at 2 μM. In the anti-inflammatory assay, 9Z-lutein and all-E-lutein exhibited higher anti-inflammatory effects than 13Z-lutein in reducing the secretion and expression of IL-8 in TNF-α induced inflammatory Caco-2 cells. Compared with the positive control, 9Z-lutein and all-E-lutein could reduce the expression of the IL-8 gene by 49% and 52%, respectively at 4 μM. This study provided a theoretical basis for the potential health benefits of Z-luteins.