A three-dimensional model of polymer electrolyte fuel cells (PEFCs) is developed to investigate multi phase flows, species transport, and electrochemical processes in fuel cells and their interactions. This two-phase model consists of conservation principles of mass, momentum, species concentration and charges, and elucidates the key physicochemical mechanisms in the constituent components of PEFCs that govern cell performance. Efforts are made to formulate two-phase transport in the anode diffusion media and its coupling with cathode flooding as well as the interaction between single- and two-phase flows. Numerical simulations are carried out to investigate multiphase flow, electrochemical activity, and transport phenomena and the intrinsic Couplings of these processes inside a fuel cell at low humidity. The results indicate that multiphase flows may exist in both anode and cathode diffusion media at low-humidity operation, and two-phase flow emerges near the outlet for co-flow configuration while is present in the middle of the fuel cell for counter-flow one. The validated numerical tools can be applied to investigate vital issues related to anode performance and degradation arising from flooding for PEFCs. Published by Elsevier B.V.