In this work, copper phthalocyanine (CuPc) was encapsulated into mesocages of MIL-101(Cr) and MIL-100(Fe) by assembling CuPc’s constitutional fractions using a deep eutectic solvent. The prepared materials, CuPc@MIL-101(Cr) and CuPc@MIL-100(Fe), were characterized by powder X-ray diffraction (PXRD), FT-IR, UV-vis and diffuse reflectance UV (DR-UV) spectroscopies, scanning electron microscopy (SEM), transmission electron microscopy (TEM), and ICP-OES spectrometry. The prepared materials were used as heterogeneous catalysts for catalytic epoxidation of styrene with molecular oxygen and also tert-butyl hydroperoxide (TBHP) as oxidants in acetonitrile as a solvent. The impact of MOFs and the role of the CuPc complex as the active species in the MOFs’ cages in the epoxidation of styrene were investigated. Among the prepared catalysts, CuPc@MIL-101(Cr) showed the best performance. The heterogeneity of the catalysts was examined by a hot filtration test and ICP-OES of the filtrates after the reaction. Spent catalysts were analyzed by PXRD, FT-IR, UV-DRS, and TEM for reusability investigation and also to further explore the heterogeneous nature of the hybrid materials. Results showed that the prepared catalysts could be recycled and used for several concoctive times without a considerable drop in activity.