Desalination systems for shale gas flowback wastewater treatment normally involve storage tanks, ion exchanges or membrane processes (e.g. ultrafiltration, reverse osmosis etc.). Note that ion exchange and membrane separation processes are typically operated semi-continuously and thus can be modeled as partitioning regeneration systems with a single inlet and two outlet streams. However, there are few researches on the synthesis of batch wastewater desalination system involving shale gas flowback wastewater treatment. This work presents a mathematical optimization model for the design and scheduling optimization of batch desalination systems for shale gas flowback wastewater treatment. A modified industrial case study is solved to illustrate the proposed approach.