The main purpose of this study was to compare the antioxidant and anticancer activities of lycopene samples with different ratios of Z-isomers. Lycopene samples containing 5%, 30%, and 55% Z-isomers were successfully prepared by using thermal treatment combined with anti-solvent crystallization. The in vitro bio-accessibility of lycopene was estimated by the determination of partition factor (PF) and the results showed that lycopene with 55% Z-isomers possessed the highest bio-accessibility. Moreover, DPPH and ABTS assays suggested that the antioxidant activity of lycopene increased with the Z-isomers content from 5% to 55%. However, lycopene inhibited the survival of human hepatocellular carcinoma cells (HepG2) in a dose and time-dependent manner. The highest inhibition of HepG2 cell lines was achieved by 55% Z-ratio of lycopene. The cell viability was 22.54% at 20 μg/mL after incubating for 24 h, the number of cells was significantly reduced and the morphology was shrunk. Furthermore, molecular docking was introduced to compare the binding ability between different lycopene isomers with Scavenger Receptor class B type I (SR-BI), and the results revealed that the affinity of (all-E)-lycopene with SR-BI was lower compared to 5Z-lycopene and 13Z-lycopene, providing the reasons for different bioavailability of the above-mentioned lycopene isomers. All the above results demonstrated that Z-isomers-rich lycopene could enhance bio-accessibility and biological functionality.