Osmotic membrane bioreactors (OMBRs) for anaerobic digestion of waste sludge have many advantages, but salt accumulation in the feed solution is a major problem. In this study, the feasibility of using flow-electrode capacitive deionization (FCDI) to mitigate salinity buildup was investigated. Three types of carbon materials, i.e., activated carbon (AC), carbon black (CB), and carbon nanotubes (CNTs), were tested as flow-electrode materials in desalination via FCDI. The results showed that, the salt removal efficiency (SRE) of CNTs was 110% higher than that of AC. Addition of CB and CNTs to 5.0 wt% AC as conductive additives at concentrations of 0.5 or 1.0 wt% synergistically enhanced the FCDI desalination performance. Cyclic voltammetry, galvanostatic charge–discharge, and electrical impendence spectroscopy showed that use of a combination of 5.0 wt% AC and 1.0 wt% CNTs gave an excellent capacitive performance, and the highest SRE, fastest average salt adsorption rate (0.84 μg cm−2 s−1), and the highest charge efficiency (85.0%) were achieved. The optimal voltage and sludge flow rate for FCDI of real OMBR sludge were 1.5 V and 80 mL min−1, respectively. In comparison with a control OMBR, a hybrid FCDI-OMBR system showed many advantages such as slower salinity buildup, alleviation of inhibition by ammonia, lower production of soluble microbial products, greater volumetric methane production, and higher net energy gains. The proposed hybrid FCDI-OMBR system provides a novel and cost-effective approach to recovering resources and energy from waste sludge or other types of biomass.