To solve the fouling issue of traditional membrane distillation (MD) technique, a newly-designed hybrid purification system integrating capacitive deionization (CDI) with MD technology was established for the organic sewage treatment in this study, namely capacitive deionizing membrane distillation (CDIMD) technology. Complexes formation via cross-linking among protein, divalent cations, and polysaccharide, an archcriminal inducing MD fouling, was remarkably alleviated in the CDIMD system considering that negatively-charged organics were clearly divided away from those divalent cations in an electric field circumstance. The CDIMD performance was deeply explored in this study focusing on the impact mechanisms of core operational parameters. An appropriate increment of feed temperature (60–65 °C) and feed flow velocity (15.72–17.82 mm/s) contributed to the anti-fouling performance of CDIMD. Considering the side reactions at voltage >1.2 v, setting working voltage at around 1.2 v seemed to be optimal for CDIMD operation. With an overall consideration of pure water production and anti-fouling performance, a properly thicker CNTs layer (40–60 μm) efficiently enhanced the fouling mitigation of CDIMD. A frequent switching of electric field direction (9/1 min) facilitated the timely regeneration of electrode and composite membranes, accordingly promoting a reliable purification of organic wastewater by CDIMD technique.