As the characteristic lengths of advanced electronic devices are approaching the atomic scale, ab initio simulation method, with fully consideration of quantum mechanical effects, becomes essential to study the quantum transport phenomenon in them. However, current widely used non-equilibrium Greens function (NEGF) approach is based on atomic basis set, which usually can only study small system with less than 1000 atoms in practice. Here we present a large-scale quantum transport simulation method using plane waves basis, based on the previously developed plane wave approach (Phys. Rev. B 72, 045417). By applying several high-efficiency parallel algorithms, such as linear-scale ground-state density function theory (DFT) algorithm, folded spectrum method, and filtering technique, we demonstrate that our new method can simulate the system with several thousands of atoms. We also use this method to study several nanowires with about 4000 copper atoms, and show how the shape and point defect affect the transport properties of them. Such quantum simulation method will be useful to investigate and design nanoscale devices, especially the on-die interconnects.