Hierarchical three-dimensional architectures of granphene-based materials with tailored microstructure and functionality exhibit unique mass transport behaviors and tunable active sites for various applications. The micro- /nanochannels in the porous structure can act as micro- /nano- reactors, which optimize the transport and conversion of contaminants. However, the size-effects of the micro- /nanochannels, which are directly related to its performance in electrochemical processes, have not been explored. Here, using lamellar-structured graphene films as electrodes, we demonstrate that the interlayer spacing (range from ∼84 nm to ∼2.44 μm) between graphene nanosheets governs the mass transport and electron transfer in electrochemical processes; subsequently influence the water decontamination performances. The microchannel (interlayer spacing = ∼2.44 μm) can provide higher active surface areas, but slow reaction kinetics. Densely packed graphene nanosheets (interlayer spacing = ∼280 nm), which possessed better electron conductivity and could provide higher surface-area-to-volume ratio in narrow nanochannels (7.14 μm-1), achieved the highest reaction kinetics. However, the ion-accessible surface area was decreased in highly dense films (interlayer spacing = ∼84 nm) due to serious interlayer stacking of graphene nanosheets, thereby leading poor reaction kinetics. These results demonstrate the size-effect of nanochannels in porous materials and highlight the importance of controlling mass transport and electron transfer for optimal electrochemical performance, enabling a deep understanding of the benefits and utilization of these hierarchical three-dimensional architectures in water purification.