Silicone-modified polyurethane (PUSX) refers to the introduction of a silicone short chain into the polyurethane chain to make it have the dual properties of silicone and polyurethane (PU). It can be used in many fields, such as coatings, films, molding products, adhesives, and so on. The use of organic solvents to achieve the fiberization of silicone-modified polyurethane has been reported. However, it is challenging to achieve the fiberization of silicone-modified polyurethane based on an environmentally friendly water solvent. Herein, we report a simple and powerful strategy to fabricate environmentally friendly waterborne silicone-modified polyurethane nanofiber membranes through the addition of polyethylene glycol (PEG) with different molecular weights using electrospinning technology and in situ doping with three crosslinking agents with different functional groups (a polyoxazoline crosslinking agent, a polycarbodiimide crosslinking agent, and a polyisocyanate crosslinking agent) combined with various heating treatment conditions. The influence of PEG molecular weight on fiber formation was explored. The morphology, structure, water resistance, and mechanical properties were analyzed regarding the effect of the introduction of silicone into PU. The effects of the type and content of crosslinking agent on the morphology and physical properties of PUSX nanofiber membranes are discussed. These results show that the introduction of silicone can improve the water resistance and high temperature resistance of waterborne PU, and the addition of a crosslinking agent can further improve the water resistance of the sample, so that the sample can maintain good morphology after immersion. Crosslinking agents with different functional groups had different effects on the mechanical properties of PUSX nanofiber membranes due to different reactions. Among them, the oxazoline crosslinking agent had a significant effect on improving tensile strength, while the isocyanate crosslinking agent had a significant effect on improving the elongation at break. The PUSX nanofiber membrane prepared in this work did not use organic solvents that were harmful to humans and the environment, and it can be used in outdoor textiles, oil–water separation, medical health, and other fields.