Superhydrophobic membranes with excellent water repellence property are good candidates for membrane distillation. In the field of polymer membranes, nonsolvent-induced phase separation (NIPS) is a common strategy to produce porous structures after the removal of solvents. Inspired by the theoretical research, we have reported a facile method to fabricate a superhydrophobic microporous membrane for desalination which combined nonsolvent-induced phase separation (NIPS) and electro-spraying. In this paper, a novel poly (vinylidene fluoride) (PVDF) membrane with a micro/nanoscale hierarchical structure has been prepared. Before electro-spraying, an appropriate amount of nonsolvent which did not cause phase separation was mixed with polymer solution. During the electro-spraying, the composition changed, and phase separation occurred owing to the volatility of solvent and nonsolvent, thus creating porous structures with high permeability and a contact angle of 152.4°, which were ideal for direct contact membrane distillation (DCMD) application. By changing the composition of three phase, different membrane morphology could be obtained. The resultant nanofibrous membranes exhibited high permeability and superhydrophobicity. The facile and scalable strategy might be applied to fabricate superhydrophobic and highly permeable membranes for desalination applications.