Nano-scale systems often display intriguing quantum mechanical effects due to system-bath couplings, i.e. polaron effect.  We demonstrate this non-trivial effect using the non-equilibrium spin-boson model  and three-level mode . To carry out the analysis, we adopt the polaron transformation as a non-perturbative method for treating open quantum systems. In the polaron frame, the equilibrium distribution presents a deviation from the canonical distribution.  Our polaron transformed Redfield equation (PTRE) bridges smoothly between the Redfield-Bloch equation in the weak coupling limit or Fermi’s golden rule in the strong coupling limit. In combination with full-counting statistics, the polaron treatment provides a unified analytical method to calculate the non-equilibrium steady state as well as the fluctuations and noise correlations, thus presenting a critical test of the thermal fluctuation theorem. The polaron analysis can be further extended to optimize the performance of light-harvesting energy transfer  and to demonstrate the phase modulation due to the Aharonov-Bohm effect . Our analysis sheds light on the coherent nature in quantum transport and is relevant for the design and control of nano-scale quantum devices.