An accurate method for three-dimensional reconstruction of microstructures is developed to analyse mass transport phenomena in microporous layers (MPLs). The proposed method involves the use of focused ion beam scanning electron microscope tomography. Numerical calculations of the structural and mass transport properties of MPLs are conducted using the reconstruction results and these results are found to be in good agreement with experimental results, demonstrating the accuracy of the new method. (C) 2017 Elsevier B.V. All rights reserved.