The spin-filter transport and magnetoresistance effects are of particular interest in the field of molecular spintronics. In this work, based on first-principles quantum transport calculations, we report on the spin-dependent transport properties of a molecular junction made of two manganese phthalocyanine (MnPc) molecules linked by single-walled carbon nanotubes. Owing to the half-metallicity of MnPc around the Fermi energy, a perfect spin-filter effect and a giant magnetoresistance effect are observed in the molecular junction. The current-voltage characteristics show nearly ohmic behavior for the junction in an anti-parallel magnetic configuration, while a very low-bias negative differential resistance effect is observed for the junction in a parallel magnetic configuration. The results are well understood from the analysis of molecular frontier orbitals, scattering states and transmission spectra. Our results provide some fundamental understanding of spin-dependent transport in molecular junctions that are useful for the design of future spintronic devices.