The two-dimensional magnetic van der Waals heterojunctions have opened unprecedented opportunities to explore new physics due to their potential for spintronic applications. Here, combing density functional theory with non-equilibrium Green’s function technique, we systematically investigate the spin-polarized transport properties of Cu/FeX2/h-BN/FeX2/Cu (X = Cl, Br, I) magnetic tunnel junctions (MTJs). It is found that the maximum tunneling magnetoresistance of Cu/FeCl2/h-BN/FeCl2/Cu, Cu/FeBr2/h-BN/FeBr2/Cu, and Cu/FeI2/h-BN/FeI2/Cu MTJs can reach 3443%, 3069%, and 1676%, respectively. In the parallel state, the resistance area products at zero bias for Cu/FeCl2/h-BN/FeCl2/Cu, Cu/FeBr2/h-BN/FeBr2/Cu, and Cu/FeI2/h-BN/FeI2/Cu MTJs are 0.92, 0.47, and 0.32 Ω⋅μm2, respectively. More interestingly, our results indicate that Cu/FeX2/h-BN/FeX2/Cu (X = Cl, Br, I) MTJs can realize spin filtering effect, while Cu/FeCl2/h-BN/FeCl2/Cu and Cu/FeI2/h-BN/FeI2/Cu MTJs exhibit negative differential resistance. Our results demonstrate that large tunneling magnetoresistance, negative differential resistance effect, low resistance area product as well as excellent spin filtering effect coexist in Cu/FeCl2/h-BN/FeCl2/Cu and Cu/FeI2/h-BN/FeI2/Cu MTJs, and that the feasible tunability of such a kind of van der Waals magnetic tunnel junctions is beneficial to designing next-generation logic devices.