In this study, a direct contact membrane module was manufactured to be used in a pilot scale membrane distillation process to treat 3 m3/day of the digestate produced from anaerobic digestion of livestock manure. In order to investigate the performance of the membrane module, permeate flux was measured with and without spacer inside the module under various condition of temperature difference and cross flow velocity (CFV) through the membrane surfaces. Flux recovery rate after chemical cleaning was also investigated by applying three different cleaning methods. Additionally, thermal energy consumption was theoretically simulated based on actual pilot plant operation conditions. As results, we observed flux of the module with spacer was almost similar to the theoretically predicted value because the installation of spacer reduced the channeling effect inside the module. Under the same operating condition, the permeate flux also increased with increasing temperature difference and CFV. As a result of chemical in-line cleaning using NaOCl and citric acid for the fouled membranes, the recovery rate was 83.7% compared to the initial flux when NaOCl was used alone, and 87% recovery rate was observed when only citric acid was used. However, in the case of using only citric acid, the permeate flux was decreased at a rapid rate. It seemed that a cleaning by NaOCl was more effective to recover the flux of membrane contaminated by the organic matter as compared to a cleaning by citric acid. The total heat energy consumption increased with increasing CFV and temperature difference across the membrane. Thus, further studies should be intensively conducted to obtain a high permeate flux while keeping the energy consumption to a minimum for a practical application of membrane distillation process to treat wastewater.