Membrane technology plays a crucial role in different separation processes such as biotechnology, pharmaceutical, and food industries, drinking water supply, and wastewater treatment. However, there is a growing concern that solvents commonly used for membrane fabrication, such as dimethylformamide (DMF), dimethylacetamide (DMAc), and 1-methyl-2-pyrrolidone (NMP), are toxic to the environment and human health. To explore the possibility of substituting these toxic solvents by less toxic or safer solvents, polymers commonly used for membrane fabrication, such as polyacrylonitrile (PAN), cellulose acetate (CA), polyethersulfone (PES), and poly(ether imide sulfone) (EXTEMTM), were dissolved in ionic liquids. Flat sheet and hollow fiber membranes were then fabricated. The thermodynamics of the polymer solutions, the kinetics of phase inversion and other factors, which resulted in significant differences in the membrane structure, compared to those of membranes fabricated from more toxic solvents, were investigated. Higher water permeance with smaller pores, unique and uniform morphologies, and narrower pore size distribution, were observed in the ionic liquid-based membranes. Furthermore, comparable performance on separation of peptides and proteins with various molecular weights was achieved with the membranes fabricated from ionic liquid solutions. In summary, we propose less hazardous polymer solutions to the environment, which can be used for the membrane fabrication with better performance and more regular morphology.