Lycopene, the aliphatic hydrocarbon carotenoid with abundant bioactivities, has instability, extremely poor water solubility, and low oral bioavailability. The study aimed to develop a highly water-soluble and practical lycopene formulation to improve the oral bioavailability and efficiency of lycopene. Environment-friendly hot-melt extrusion (HME) technique was applied to fabricate lycopene-cyclodextrin-polyethylene glycol 6000 (PEG 6000) ternary systems, which possessed highly aqueous solubility (897.665 μg mL), almost 32-fold higher than that of the reported lycopene binary inclusion (27.1 ± 3.2 μg mL). The dissolution rate was significantly accelerated compared to pure lycopene. The molecular mechanism was further investigated by the integrated experimental and modeling tools. Molecular dynamics (MD) simulation revealed lycopene molecule was wrapped within the aggregates of hydroxypropyl-beta-cyclodextrin (HP-β-CD) and PEG 6000 through extensive hydrogen bond interactions, which was experimentally validated by DSC, XRD, and FTIR spectrum analysis. The third component PEG 6000 facilitated the process of HME and augmented hydrogen bond interactions with HP-β-CD. Moreover, lycopene inclusions exhibited significant antitumor activity via inhibiting cell proliferation and inducing apoptosis. The pharmacokinetic studies showed the relative bioavailability of lycopene ternary preparation was up to 313.08% and the C was 4.9-fold higher than that of the marketed tablet. In conclusion, the lycopene cyclodextrin ternary formulation developed by the modified HME techniques is suitable for industrial production, while PEG 6000 plays a vital part in the multicomponent systems to increase solubility, dissolution rate, and oral bioavailability of lycopene. The combination of experimental and computational tools is able to benefit the development of multicomponent formulations accurately and effectively.