Fluoropolymer membranes are applied in membrane operations such as membrane distillation and membrane crystallization where hydrophobic porous membranes act as a physical barrier separating two phases. Due to their hydrophobic nature, only gaseous molecules are allowed to pass through the membrane and are collected on the permeate side, while the aqueous solution cannot penetrate. However, these two processes suffer problems such as membrane wetting, fouling or scaling. Membrane wetting is a common and undesired phenomenon, which is caused by the loss of hydrophobicity of the porous membrane employed. This greatly affects the mass transfer efficiency and separation efficiency. Simultaneously, membrane fouling occurs, along with membrane wetting and scaling, which greatly reduces the lifespan of the membranes. Therefore, strategies to improve the hydrophobicity of membranes have been widely investigated by researchers. In this direction, hydrophobic fluoropolymer membrane materials are employed more and more for membrane distillation and membrane crystallization thanks to their high chemical and thermal resistance. This paper summarizes different preparation methods of these fluoropolymer membrane, such as non-solvent-induced phase separation (NIPS), thermally-induced phase separation (TIPS), vapor-induced phase separation (VIPS), etc. Hydrophobic modification methods, including surface coating, surface grafting and blending, etc., are also introduced. Moreover, the research advances on the application of less toxic solvents for preparing these membranes are herein reviewed. This review aims to provide guidance to researchers for their future membrane development in membrane distillation and membrane crystallization, using fluoropolymer materials.