Many studies have been conducted on flow-electrode capacitive deionization (FCDI), by which the limited ion adsorption capacity per unit cell can be extended, and which can be applied to high-salinity water treatment. Especially, using low-cost ceramic filters as three-dimensional (3D) electrode structure for FCDI is possible, instead of stacking the unit cells for scale-up. However, using ceramic partition walls as spacer can affect water flow and ion transport due to their thickness and porosity. Furthermore, the integrated membrane-spacer-assembly (MSA) having a membrane-coated spacer is more suitable for 3D electrode structure than a separated MSA having a spacer sandwiched between membranes. Herein we investigated the effects of the thickness and porosity of plate-type porous ceramic spacers on the electrochemical properties of the cell and compared the electrochemical properties of separated MSA with those of integrated MSA. Spacer porosity was found to have a larger effect than spacer thickness. Integrated MSA had larger resistance and lower capacitance than separated MSA, leading to lower desalination performance. It was attributed to the change in physical properties of the spacer induced by coating and the difference in ion exchange capacity of the coated membrane itself.