Two-dimensional (2D) layered materials have an atomically thin and flat nature which makes it an ultimate candidate for spintronic devices. The spin-valve junctions (SVJs), composed of 2D materials, have been recognized as unique features of spin transport polarization. However, the magnetotransport properties of SVJs are highly influenced by the type of intervening layer (spacer) inserted between the ferromagnetic materials (FMs). In this situation, the spin filtering effect at the interfaces plays a critical role in the observation of the magnetoresistance (MR) of such magnetic structures, which can be improved by using promising hybrid structure. Here, we report MR of bilayer graphene (BLG), single-layer MoSe2 (SL-MoSe2), and BLG/SL-MoSe2 heterostack SVJs. However, before annealing, BLG and SL-MoSe2 SVJs demonstrate positive MR, but after annealing, BLG reverses its polarity while the SL-MoSe2 maintains its polarity and demonstrated stable positive spin polarizations at both interfaces due to meager doping effect of ferromagnetic (FM) contacts. Further, Co/BLG/SL-MoSe2/NiFe determines positive MR, i.e., ~ 1.71% and ~ 1.86% at T = 4 K before and after annealing, respectively. On the contrary, NiFe/BLG/SL-MoSe2/Co SVJs showed positive MR before annealing and subsequently reversed its MR sign after annealing due to the proximity-induced effect of metals doping with graphene. The obtained results can be useful to comprehend the origin of polarity and the selection of non-magnetic material (spacer) for magnetotransport properties. Thus, this study established a new paragon for novel spintronic applications.