The architecture and performance of microbial desalination cell (MDC) have been significantly improved in the past few years. However, the application of MDC is still limited in a scope of small-scale (milliliter) reactors and high-salinity-water desalination. In this study, a large-scale (>10 L) stacked MDC packed with mixed ion-exchange resins was fabricated and operated in the batch mode with a salt concentration of 0.5 g/L NaCl, a typical level of domestic wastewater. With circulation flow rate of 80 mL/min, the stacked resin-packed MDC (SR-MDC) achieved a desalination efficiency of 95.8% and a final effluent concentration of 0.02 g/L in 12 h, which is comparable with the effluent quality of reverse osmosis in terms of salinity. Moreover, the SR-MDC kept a stable desalination performance (>93%) when concentrate volume decreased from 2.4 to 0.1 L (diluate/concentrate volume ratio increased from 1:1 to 1:0.04), where only 0.875 L of nonfresh water was consumed to desalinate 1 L of saline water. In addition, the SR-MDC achieved a considerable desalination rate (95.4 mg/h), suggesting a promising application for secondary effluent desalination through deriving biochemical electricity from wastewater.