Capacitive deionization (CDI) is a promising desalination process, but conventional static electrode CDI operates by sequentially cycling through charging and discharging to produce fresh and concentrated water, respectively. However, an effective continuous operation is desirable for optimized system operation. Here, we report a semi continuous desalination process with a novel modified CDI cell architecture using a multi-channel flow stream and ion exchange membranes (MC-MCDI). This MC-MCDI consists of two channels including side and middle channels with a pair of cation and anion ion exchange membranes where the feed streams can be separately distributed without mixing. The MC-MCDI design allows semi-continuous production of clean water since the separated middle and side channels are alternately desalinated and regenerated: one channel is being desalinated while the other channel is regenerated. Therefore, the cell can produce clean water during both charging and discharging, enabling semi-continuous operation. In addition, with the benefit from similar cell configuration with membrane CDI, the MC-MCDI design exhibits a high salt adsorption capacity (SAC) of 22 +/- 2 mg/g and charge efficiency of 90 +/- 2% at middle and side channels during charging and discharging with reverse voltage operation (cell voltage of + 1.2 V vs.- 1.2 V).