Membrane distillation requires a lower operation temperature than other separation processes. It is also able to use low-grade thermal energy. In this study, an integrated design method that utilizes a membrane distillation (MD) system to produce pure water is presented. This method is the integration of the heat exchanger network (HEN) into the MD system, and it uses the waste heat from HEN as the energy source of the MD process so as to greatly reduce the water cost. In this proposed method, a multistage MD system is designed to generate the optimal system structure and operating conditions. Then the output and input MD streams are merged into the existing HEN so that the energy cost of pure water can be determined by redesigning the HEN with the trans-shipment models. The efficiency of the proposed method is demonstrated through an industrial case.