A membrane-based desalination system under consideration for shale gas fracturing flowback wastewater treatment involves ultrafiltration (UF), reverse osmosis (RO), and storage tanks. The membrane unit (UF, RO) consists of online washing, operation, and offline chemical washing sub-units. These sub-units operate in semi-continuous mode and have the similar characteristics as batch water-using processes. Based on their semi-continuous behaviors, the models of UF and RO sub-units are developed. The objective is to maximize the total water production ratio and profit while minimizing storage tank capacity. Three nonlinear programming optimization models are developed for an optimal design of the UF-RO treatment system for shale gas fracturing flowback wastewater. Two scenarios, fixed schedule and fixed operating period, for UF/RO treatment sub-units are investigated. Results show that with the increasing of the operation duration of treatment sub-units, the water production ratio and profit will increase. The schedule of treatment sub-units has significant impact on the water storage profiles, without adversely affecting the water production ratio. The proposed approach can guide the design of the UF-RO desalination system.