Developing a practical and efficient method for the Z-isomerization of lycopene is essential, as the Z-isomers exhibit higher biological activity and bioavailability compared to the all-E-isomer. The aim of this study was to develop an innovative approach to induce thermal Z-isomerization of (all-E)-lycopene by utilizing a dual-media system consisting of oil and ethanol in conjunction with a heat-pressure process. Specifically, the effects of reaction temperature, initial reaction pressure, ethanol volume ratio, and reaction time were investigated. The novel reaction system effectively facilitated the Z-isomerization of (all-E)-lycopene. For instance, when subjected to a reaction at 120 °C for 30 min, the total Z-isomer ratio surpassed 66%. FTIR, DSC, and XRD confirmed the presence of Z-isomer-rich lycopene dispersed in oil in an amorphous state and with a lower melting point. Moreover, an evaluation of the stability of Z-isomer-rich lycopene in olive oil revealed a decreasing trend in both lycopene concentration and total Z-isomer ratio with increasing temperature and storage time. Notably, among the lycopene isomers, (5Z)-lycopene showed the greatest stability compared to other isomers of lycopene. This eco-friendly and efficient isomerization technology is a useful approach for producing Z-isomer-rich lycopene materials.