Nanosized Cu2O catalysts with precisely controlled bud-to-blooming flower shapes are synthesised using modified polyol method. The evolution of the shape when the catalysts are applied to the gas diffusion electrodes improves the key factors influencing the catalyst layer, e.g. volume porosity and triple-phase boundary contact areas. Numerical and experimental studies revealed increased reactant molar concentration and improved CO2 mass transfer due to the structural changes, which influenced the electrochemical CO2 reduction reaction (eCO2RR). The fully bloomed Cu2O nanoflower catalyst, combined with the two-dimensional (2D) structured graphene sheet, formed a catalyst layer with scaffolding structure that exhibited the highest Faradaic efficiency (FE) of 93.20% towards CO at an applied potential of −1.0 V vs. RHE in 1M KOH. These findings established the relationship between the catalyst layer properties and mass transfer, based on which we could describe the effect of the structural design of the catalyst layer on the eCO2RR performance.