Molecule-substrate interfaces are ubiquitous in nanoscale functional materials and energy related applications. Characterizing the electronic structure at molecule-substrate interfaces, especially the energy level alignment between molecular frontier orbitals and the Fermi level of the substrate, is crucial for understanding interfacial charge dynamics. Density functional theory (DFT) has been successful in computing binding geometries and adsorption energies, but much less successful in predicting level alignments. This is because the latter depends on quasiparticle excitation energies, typically believed to be outside the reach of DFT. Many-body perturbation theory, such as the GW approach, provides a formal theoretical framework for quasiparticle energies, but the computational cost for typical interfaces is high. In this talk, I will introduce two methodological advancements for accurate and efficient calculations of level alignments at weakly coupled molecule-substrate interfaces: (1) an optimally tuned range-separated hybrid functional, taking into account the substrate screening effect via the image-charge model; and (2) a novel GW approach employing the additivity of the Kohn-Sham polarizability for the interface, which significantly reduces the computational cost compared to direct GW calculations.