The desalination treatment of shale gas fracturing flowback wastewater can be used for the wastewater reuse and reasonable discharge. The modeling and energy efficiency analysis of desalination treatment process can guide the process optimization and efficient operation. The membrane-based desalination process of shale gas fracturing flowback wastewater includes the pretreatment process (electrocoagulation and ultrafiltration) and reverse osmosis. For the membrane module of reverse osmosis unit, the solution-diffusion model is adopted to describe the mass transfer process. Furthermore, the water permeability constant and the mass transfer coefficient of salt were calculated based on the experimental data. Finally, the energy efficiency and economic evaluation model is established, and the influence of the energy recovery system on the economy and energy efficiency of the desalination process is considered. The results show that the total energy consumption is reduced by 20.45%, and the annual operation cost of the pump is reduced by 15.29% with the help of energy recovery system.