The resistance at the diffusion boundary layer limits ion transport through membrane (counter-ionic) in electro-electrodialysis (EED), which are addressed through novel design of flow promoter (spacer), but increased pressure drop in the flow channel and power consumption are major rudiments. This report investigates casting of template based micro molded membranes containing cylinder, square-pillar, and rectangular-pillar corrugations and their application in EED setup without spacer. Square-pillar showed higher ion transport relative to rectangular-pillar and cylinder, which was supported by increased surface area, and reduced boundary layer thickness. For height optimization of square pillar corrugation, corrugated membranes containing pillars of five different heights: 50, 75, 100, 125 and 150 μm were synthesized and tested for using EED setup, where 100 μm height showed better ion transport. Limited ion transport with corrugation height above 100 μm resulted lower concentration of NaOH requiring higher energy. Corrugated membrane with two different arrangements of square pillars: linear and staggered were tested keeping their height same (100 μm), where staggered arrangement showed better ion transport. Direction of applied current facing flat and corrugated performed differently in ion transport, and the latter performed better due to reduced boundary layer resistance. All EED experiments were conducted with industrial green liquor feed to obtain NaOH (mol·L−1) as product, where current density, flowrate and duration were kept unchanged. NaOH recovery, Current efficiency, and energy consumption estimates with each configuration was supported through velocity profiles obtained by solving equation of motion and continuity using COMSOL multiphysics software. Combine effect of turbulence creations due to corrugation, surface area increment and boundary layer thickness control the ion transport.