Charge transport processes at the nanoscale lies at the heart of electronic, photovoltaic, and thermoelectric devices. When charge is transferred in a molecular system, its environments, in the form of electrical contacts, internal nuclear motion, solvent and electromagnetic fields fundamentally influence its behavior, posing a great challenge for theoretical modelings. In this talk, I will present our recent attempt, termed generalized input-output method, to address aforementioned effects on charge transfer in molecular junctions. This talk will cover the essential formalism, its implementation as well as applications, with a special focus on new understandings gained from the approach about electron-vibration effects in molecular transport junctions .