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Two-dimensional (2D) layered materials and their heterostructures have opened a new avenue for next-generation spintronic applications, benefited by their unique electronic properties and high crystallinity with an atomically flat surface. Here, we report magnetoresistance of vertical magnetic spin-valve devices with multi-layer (ML) MoSe2 and its heterostructures with few-layer graphene (FLG). We employed a micro-fabrication procedure to form ultraclean ferromagnetic–non-magnetic–ferromagnetic interfaces to elucidate the intrinsic spin-transferring mechanism through both an individual material and combinations of 2D layered materials. However, it is revealed that the polarity of tunneling magnetoresistance (TMR) is independent of non-magnetic spacers whether the spin valve is composed of a single material or a hybrid structure, but it strongly depends on the interfaces between ferromagnetics (FMs) and 2D materials. We observed positive spin polarizations in ML-MoSe2 and FLG/ML-MoSe2/FLG tunnel junctions, whereas spin-valve devices comprised of FLG/ML-MoSe2 showed a reversed spin polarization and demonstrated a negative TMR. Importantly, in Co/FLG/ML-MoSe2/FLG/NiFe devices, the polarization of spin carriers in the FM/FLG interface remained conserved during tunneling through MoSe2 flakes in spin-transferring events, which is understandable by Julliere’s model. In addition, large TMR values are investigated at low temperatures, whereas at high temperatures, the TMR ratios are deteriorated. Furthermore, the large values of driving ac-current also quenched the amplitude of TMR signals. Therefore, our observations suggest that the microscopic spin-transferring mechanism between ferromagnetic metals and 2D materials played a momentous role in spin-transferring phenomena in vertical magnetic spin-valve junctions.